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1

The Genographic Project Public Participation Mitochondrial DNA Database  

PubMed Central

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool. PMID:17604454

Behar, Doron M; Rosset, Saharon; Blue-Smith, Jason; Balanovsky, Oleg; Tzur, Shay; Comas, David; Mitchell, R. John; Quintana-Murci, Lluis; Tyler-Smith, Chris; Wells, R. Spencer

2007-01-01

2

A protocol for species delineation of public DNA databases, applied to the Insecta.  

PubMed

Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L × S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity. PMID:24929897

Chesters, Douglas; Zhu, Chao-Dong

2014-09-01

3

NCCDPHP PUBLICATION DATABASE  

EPA Science Inventory

This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

4

The National DNA Database  

Microsoft Academic Search

Over the last two years the Forensic Science Service (FSS) has developed and put into operation a National DNA Database that has analysed samples from individuals suspected of crime and stains from scenes of crime. It has provided more than 2200 links between individuals and scenes and 1200 links between scenes of crime. It uses an STR SGM (second generation

David J Werrett

1997-01-01

5

Determining the identifiability of DNA database entries.  

PubMed Central

CleanGene is a software program that helps determine the identifiability of sequenced DNA, independent of any explicit demographics or identifiers maintained with the DNA. The program computes the likelihood that the release of DNA database entries could be related to specific individuals that are the subjects of the data. The engine within CleanGene relies on publicly available health care data and on knowledge of particular diseases to help relate identified individuals to DNA entries. Over 20 diseases, ranging over ataxias, blood diseases, and sex-linked mutations are accounted for, with 98-100% of individuals found identifiable. We assume the genetic material is released in a linear sequencing format from an individual's genome. CleanGene and its related experiments are useful tools for any institution seeking to provide anonymous genetic material for research purposes. PMID:11079941

Malin, B.; Sweeney, L.

2000-01-01

6

AIDS PUBLIC INFORMATION DATABASE  

EPA Science Inventory

The AIDS Public Information Data Set is computer software designed to run on a Microsoft Windows microcomputer, and contains information abstracted from acquired immunodeficiency syndrome (AIDS) cases reported in the United States. The data set is created by the Division of HIV/A...

7

Database Support for Research in Public Administration  

ERIC Educational Resources Information Center

This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases

Tucker, James Cory

2005-01-01

8

Towards Privacy Preserving of Forensic DNA Databases  

E-print Network

Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

Liu, Sanmin

2012-02-14

9

Short Tandem Repeat DNA Internet Database  

National Institute of Standards and Technology Data Gateway

SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

10

REPAIRtoire—a database of DNA repair pathways  

PubMed Central

REPAIRtoire is the first comprehensive database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire provides also links to publications and external databases. REPAIRtoire contains information about eight main DNA damage checkpoint, repair and tolerance pathways: DNA damage signaling, direct reversal repair, base excision repair, nucleotide excision repair, mismatch repair, homologous recombination repair, nonhomologous end-joining and translesion synthesis. The pathway/protein dataset is currently limited to three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease. In addition, a tool for drawing custom DNA–protein complexes is available online. REPAIRtoire is freely available and can be accessed at http://repairtoire.genesilico.pl/. PMID:21051355

Milanowska, Kaja; Krwawicz, Joanna; Papaj, Grzegorz; Kosi?ski, Jan; Poleszak, Katarzyna; Lesiak, Justyna; Osi?ska, Ewelina; Rother, Kristian; Bujnicki, Janusz M.

2011-01-01

11

Plant rDNA database: update and new features  

PubMed Central

The Plant rDNA database (www.plantrdnadatabase.com) is an open access online resource providing detailed information on numbers, structures and positions of 5S and 18S-5.8S-26S (35S) ribosomal DNA loci. The data have been obtained from >600 publications on plant molecular cytogenetics, mostly based on fluorescent in situ hybridization (FISH). This edition of the database contains information on 1609 species derived from 2839 records, which means an expansion of 55.76 and 94.45%, respectively. It holds the data for angiosperms, gymnosperms, bryophytes and pteridophytes available as of June 2013. Information from publications reporting data for a single rDNA (either 5S or 35S alone) and annotation regarding transcriptional activity of 35S loci now appears in the database. Preliminary analyses suggest greater variability in the number of rDNA loci in gymnosperms than in angiosperms. New applications provide ideograms of the species showing the positions of rDNA loci as well as a visual representation of their genome sizes. We have also introduced other features to boost the usability of the Web interface, such as an application for convenient data export and a new section with rDNA–FISH-related information (mostly detailing protocols and reagents). In addition, we upgraded and/or proofread tabs and links and modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments. Database URL: http://www.plantrdnadatabase.com PMID:24980131

Garcia, Sňnia; Gálvez, Francisco; Gras, Airy; Kova?ík, Aleš; Garnatje, Teresa

2014-01-01

12

Publications of Australian LIS Academics in Databases  

ERIC Educational Resources Information Center

This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

2011-01-01

13

MitoBreak: the mitochondrial DNA breakpoints database  

PubMed Central

Mitochondrial DNA (mtDNA) rearrangements are key events in the development of many diseases. Investigations of mtDNA regions affected by rearrangements (i.e. breakpoints) can lead to important discoveries about rearrangement mechanisms and can offer important clues about the causes of mitochondrial diseases. Here, we present the mitochondrial DNA breakpoints database (MitoBreak; http://mitobreak.portugene.com), a free, web-accessible comprehensive list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially duplicated (duplications) and linear mtDNAs. Currently, MitoBreak contains >1400 mtDNA rearrangements from seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Drosophila melanogaster, Caenorhabditis elegans and Podospora anserina) and their associated phenotypic information collected from nearly 400 publications. The database allows researchers to perform multiple types of data analyses through user-friendly interfaces with full or partial datasets. It also permits the download of curated data and the submission of new mtDNA rearrangements. For each reported case, MitoBreak also documents the precise breakpoint positions, junction sequences, disease or associated symptoms and links to the related publications, providing a useful resource to study the causes and consequences of mtDNA structural alterations. PMID:24170808

Damas, Joana; Carneiro, Joăo; Amorim, António; Pereira, Filipe

2014-01-01

14

Publication Kind Codes in STN Patent Databases  

E-print Network

Publication Kind Codes in STN Patent Databases Dokumentenart-Codes in STN-Patentdatenbanken Imprint Abstracts (CAPLUS), Chemical Abstracts (CAPLUS), Derwent World Patents Index (DWPI), and Derwent World Patents Index (DWPI)und INPADOCDB INPADOCDB international patent databases, together with a short

Hoffmann, Armin

15

Online Database Searching in Smaller Public Libraries.  

ERIC Educational Resources Information Center

Online database searching experiences of nine Illinois public libraries--Arlington Heights, Deerfield, Elk Grove Village, Evanston, Glenview, Northbrook, Schaumburg Township, Waukegan, Wilmette--are discussed, noting search costs, user charges, popular databases, library acquisition, interaction with users, and staff training. Three sources are…

Roose, Tina

1983-01-01

16

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database  

E-print Network

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database Wellcome Trust response on the important topic of the forensic use of DNA and the National DNA Database (NDNAD). Given the Trust Assembly; "Forensic DNA Databasing: A European perspective" - a biomedical ethics grant to Professor Robin

Rambaut, Andrew

17

An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database)  

PubMed Central

Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. Description We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. Conclusions This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry. PMID:20576098

2010-01-01

18

Angiosperm DNA C-Values Database  

NSDL National Science Digital Library

The 1992 Global Convention on Biological Diversity (Rio de Janeiro) specified the need to make biodiversity data available "despite imperfections, rather than holding back information until more polished products are completed." Few organizations have done so. This Royal Botanic Gardens (Kew, UK) genome biodiversity database is one valuable exception. Founded in 1759, the Royal Botanic Gardens, Kew has built its unique collections which now include 6 million dried plant specimens - covering 90% of the world's plant species; 40,000 living plant taxa - estimated as 10% of the world's flora; and 80,000 fungi and artifacts of plant origin. Known best among botanists as a global resource for definitively identifying, classifying, and naming plants and fungi, Kew also maintains this database on DNA C-values. To access this free, searchable database, the user must provide an email address as well as the genus of interest; search results include Taxon, Family, 4C DNA amount (pg), and entry number/reference citation, listed separately for each species.

19

IRSS Public Opinion Poll Question Database  

NSDL National Science Digital Library

This database, constructed by the Institute for Research in Social Science (IRSS) at the University of North Carolina at Chapel Hill, allows researchers to conduct keyword searches on questions derived from a collection of public opinion polls, dating from the 1960s to the present. Query results display the full text of the poll questions, information about the studies, and, in many searches, frequency distributions. Users also have the option to view the full catalog record and download data from selected studies from the data archive. The IRSS Public Opinion Poll Question Database is an excellent resource for researchers who are developing "questions for their own studies, as well as for users interested in frequencies or in locating particular variables for statistical analysis."

20

[Integrated DNA barcoding database for identifying Chinese animal medicine].  

PubMed

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources. PMID:25244735

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

21

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences  

Federal Register 2010, 2011, 2012, 2013, 2014

...Information Database: Notice of Public Web Conferences AGENCY: Consumer Product Safety...or ``we'') is announcing two Web conferences to demonstrate to interested...information database (``Database''). The Web conferences will be webcast live from...

2011-01-07

22

MICA: desktop software for comprehensive searching of DNA databases  

PubMed Central

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

Stokes, William A; Glick, Benjamin S

2006-01-01

23

Searching mixed DNA profiles directly against profile databases.  

PubMed

DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. PMID:24528588

Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

2014-03-01

24

DNA algorithms of implementing biomolecular databases on a biological computer.  

PubMed

In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases. PMID:25343766

Chang, Weng-Long; Vasilakos, Athanasios V

2015-01-01

25

Exploration of the Chemical Space of Public Genomic Databases  

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. ...

26

75 FR 29155 - Publicly Available Consumer Product Safety Information Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...have collected in our database library, which will...contact/account management, e-mail communication...report to the public database does the system checks...available and searchable database. As such, the proposed...review by the Office of Management and Budget (OMB)...

2010-05-24

27

MethHC: a database of DNA methylation and gene expression in human cancer  

PubMed Central

We present MethHC (http://MethHC.mbc.nctu.edu.tw), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data. PMID:25398901

Huang, Wei-Yun; Hsu, Sheng-Da; Huang, Hsi-Yuan; Sun, Yi-Ming; Chou, Chih-Hung; Weng, Shun-Long; Huang, Hsien-Da

2015-01-01

28

The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease.  

PubMed

A recent review identified 60 common inherited renal diseases caused by DNA variants in 132 different genes. These diseases can be diagnosed with DNA sequencing, but each gene probably also has a thousand normal variants. Many more normal variants have been characterised by individual laboratories than are reported in the literature or found in publicly accessible collections. At present, testing laboratories must assess each novel change they identify for pathogenicity, even when this has been done elsewhere previously, and the distinction between normal and disease-associated variants is particularly an issue with the recent surge in exomic sequencing and gene discovery projects. The Human Variome Project recommends the establishment of gene-specific DNA variant databases to facilitate the sharing of DNA variants and decisions about likely disease causation. Databases improve diagnostic accuracy and testing efficiency, and reduce costs. They also help with genotype-phenotype correlations and predictive algorithms. The Human Variome Project advocates databases that use standardised descriptions, are up-to-date, include clinical information and are freely available. Currently, the genes affected in the most common inherited renal diseases correspond to 350 different variant databases, many of which are incomplete or have insufficient clinical details for genotype-phenotype correlations. Assistance is needed from nephrologists to maximise the usefulness of these databases for the diagnosis and management of inherited renal disease. PMID:25384529

Savige, Judy; Dalgleish, Raymond; Cotton, Richard Gh; den Dunnen, Johan T; Macrae, Finlay; Povey, Sue

2014-11-11

29

Cryptographic Approaches to Provacy in Forensic DNA Databases  

Microsoft Academic Search

Advances in DNA sequencing technology and human genetics are leading to the availabilityof inexpensive genetic tests, notably tests for individual predisposition to certain diseases. Whilesuch information is often valuable, its availability has raised serious concerns over the privacyof genetic information. These concerns are further heightened when genetic information isgathered into databases. We study access control for one class of such

Philip Bohannon; Markus Jakobsson; Sukamol Srikwan

2000-01-01

30

DNAVaxDB: the first web-based DNA vaccine database and its data analysis.  

PubMed

Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development. PMID:25104313

Racz, Rebecca; Li, Xinna; Patel, Mukti; Xiang, Zuoshuang; He, Yongqun

2014-01-01

31

Choice of population database for forensic DNA profile analysis.  

PubMed

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. PMID:25498938

Steele, Christopher D; Balding, David J

2014-12-01

32

Toward Privacy in Public Databases Shuchi Chawla1  

E-print Network

Toward Privacy in Public Databases Shuchi Chawla1 , Cynthia Dwork2 , Frank McSherry2 , Adam Smith3,mcsherry}@microsoft.com 3 Weizmann Institute of Science, adam.smith@weizmann.ac.il 4 University of California, Berkeley ARO Grant DAAD19-00-1-0177. #12;2 S. Chawla, C. Dwork, F. McSherry, A. Smith and H. Wee sanitization

Chawla, Shuchi

33

Building a Faculty Publications Database: A Case Study  

ERIC Educational Resources Information Center

This case study shares the experience of building an in-house faculty publications database that was spearheaded by the Touro College and University System library in 2010. The project began with the intention of contributing to the college by collecting the research accomplishments of our faculty and staff, thereby also increasing library…

Tabaei, Sara; Schaffer, Yitzchak; McMurray, Gregory; Simon, Bashe

2013-01-01

34

Dfam: a database of repetitive DNA based on profile hidden Markov models  

E-print Network

Dfam: a database of repetitive DNA based on profile hidden Markov models Travis J. Wheeler1 not been possible to apply profile HMM search to TE annotation because DNA search was too slow. However a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large

Eddy, Sean

35

A publication database for optical long baseline interferometry  

NASA Astrophysics Data System (ADS)

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

Malbet, Fabien; Mella, Guillaume; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

2010-07-01

36

Pathway Analysis for Drug Repositioning Based on Public Database Mining  

PubMed Central

Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public databases including the MMDB, PubChem BioAssay, GEO DataSets, and the BioSystems databases. Entrez E-Utilities were applied, and in-house Ruby scripts were developed for data retrieval and pathway analysis to identify and evaluate relevant pathways common to the retrieved drug targets. Pathways pertinent to clinical uses or MOAs were obtained for most drugs. Interestingly, some drugs identified pathways responsible for other diseases than their current therapeutic uses, and these pathways were verified retrospectively by in vitro tests, in vivo tests, or clinical trials. The pathway enrichment analysis based on drug target information from public databases could provide a novel approach for elucidating drug MOAs and repositioning, therefore benefiting the discovery of new therapeutic treatments for diseases. PMID:24460210

2015-01-01

37

Abundant human DNA contamination identified in non-primate genome databases.  

PubMed

During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species. Using a primate specific SINE, AluY, we screened 2,749 non-primate public databases from NCBI, Ensembl, JGI, and UCSC and have found 492 to be contaminated with human sequence. These represent species ranging from bacteria (B. cereus) to plants (Z. mays) to fish (D. rerio) with examples found from most phyla. The identification of such extensive contamination of human sequence across databases and sequence types warrants caution among the sequencing community in future sequencing efforts, such as human re-sequencing. We discuss issues this may raise as well as present data that gives insight as to how this may be occurring. PMID:21358816

Longo, Mark S; O'Neill, Michael J; O'Neill, Rachel J

2011-01-01

38

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.  

PubMed

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone. PMID:24214955

Yang, Lin; Zhou, Tianyin; Dror, Iris; Mathelier, Anthony; Wasserman, Wyeth W; Gordân, Raluca; Rohs, Remo

2014-01-01

39

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS  

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models Ann M. Richard US Environmental Protection Agency, Research Triangle Park, NC, USA Distributed: Decentralized set of standardized, field-delimited databases,...

40

75 FR 76831 - Publicly Available Consumer Product Safety Information Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...electronic form specifically developed to collect the report of harm in the Database. Proposed Sec. 1102...we have maintained a database on consumer product...for reports of harm developed for the Database, both online and...

2010-12-09

41

Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models  

E-print Network

1 Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models Travis J. Wheeler. To date, it has not been possible to apply profile HMM search to TE annotation because DNA search was too brings the power of profile HMMs to DNA homology search with good speed (~10x slower than blastn

Eddy, Sean

42

Evaluating DNA profile evidence when the suspect is identified through a database search  

Microsoft Academic Search

ABSTRACT: The paper is concerned with the strength of DNA evidence when a suspect is identified via a search through a database of the DNA profiles of known,individuals. Consideration of the appropriate likelihood ratio shows that in this setting the DNA evidence is (slightly) stronger than when,a suspect is identified by other means, subsequently profiled, and found to match. The

Dj Balding; P Donnelly

1996-01-01

43

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives  

PubMed Central

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations. PMID:21674821

Marjanovi?, Damir; Konjhodži?, Rijad; Butorac, Sara Sanela; Drobni?, Katja; Merkaš, Siniša; Lauc, Gordan; Primorac, Damir; An?elinovi?, Šimun; Milosavljevi?, Mladen; Karan, Željko; Vidovi?, Stojko; Stojkovi?, Oliver; Pani?, Bojana; Vu?eti? Dragovi?, An?elka; Kova?evi?, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

2011-01-01

44

75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database  

Federal Register 2010, 2011, 2012, 2013, 2014

...non-proprietary in the single-family database. i. Single-Family Data...unknown) in the single-family database. j. Single-Family Data...type code of ``61 = asset management refinance'' is not applicable...414-6924. VI. Order Public Use Database for Enterprise Mortgage...

2010-07-15

45

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase  

PubMed Central

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism. PMID:19640306

2009-01-01

46

Databases and Bioinformatics Tools for the Study of DNA Repair  

PubMed Central

DNA is continuously exposed to many different damaging agents such as environmental chemicals, UV light, ionizing radiation, and reactive cellular metabolites. DNA lesions can result in different phenotypical consequences ranging from a number of diseases, including cancer, to cellular malfunction, cell death, or aging. To counteract the deleterious effects of DNA damage, cells have developed various repair systems, including biochemical pathways responsible for the removal of single-strand lesions such as base excision repair (BER) and nucleotide excision repair (NER) or specialized polymerases temporarily taking over lesion-arrested DNA polymerases during the S phase in translesion synthesis (TLS). There are also other mechanisms of DNA repair such as homologous recombination repair (HRR), nonhomologous end-joining repair (NHEJ), or DNA damage response system (DDR). This paper reviews bioinformatics resources specialized in disseminating information about DNA repair pathways, proteins involved in repair mechanisms, damaging agents, and DNA lesions. PMID:22091405

Milanowska, Kaja; Rother, Kristian; Bujnicki, Janusz M.

2011-01-01

47

The effect of wild card designations and rare alleles in forensic DNA database searches.  

PubMed

Forensic DNA databases are powerful tools used for the identification of persons of interest in criminal investigations. Typically, they consist of two parts: (1) a database containing DNA profiles of known individuals and (2) a database of DNA profiles associated with crime scenes. The risk of adventitious or chance matches between crimes and innocent people increases as the number of profiles within a database grows and more data is shared between various forensic DNA databases, e.g. from different jurisdictions. The DNA profiles obtained from crime scenes are often partial because crime samples may be compromised in quantity or quality. When an individual's profile cannot be resolved from a DNA mixture, ambiguity is introduced. A wild card, F, may be used in place of an allele that has dropped out or when an ambiguous profile is resolved from a DNA mixture. Variant alleles that do not correspond to any marker in the allelic ladder or appear above or below the extent of the allelic ladder range are assigned the allele designation R for rare allele. R alleles are position specific with respect to the observed/unambiguous allele. The F and R designations are made when the exact genotype has not been determined. The F and R designation are treated as wild cards for searching, which results in increased chance of adventitious matches. We investigated the probability of adventitious matches given these two types of wild cards. PMID:25576850

Tvedebrink, Torben; Bright, Jo-Anne; Buckleton, John S; Curran, James M; Morling, Niels

2015-05-01

48

The EpiSLI Database: A Publicly Available Database on Speech and Language  

ERIC Educational Resources Information Center

Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

Tomblin, J. Bruce

2010-01-01

49

DNA Fingerprint Database for Crapemyrtle Cultivar Identification, Hybrid Verification, and Parentage Analysis  

Technology Transfer Automated Retrieval System (TEKTRAN)

The objective of this study was to create DNA fingerprints for the Razzle Dazzle® crape myrtle series using simple sequence repeat (SSR) markers, and compare them with the DNA fingerprints of a database made up of over 50 popular crape myrtle cultivars currently available in the trade. Data consiste...

50

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.  

PubMed

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma. PMID:23860041

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

51

Construction and use of a computerized DNA fingerprint database for lactic acid bacteria from silage.  

PubMed

Efficient selection of new silage inoculant strains from a collection of over 10,000 isolates of lactic acid bacteria (LAB) requires excellent strain discrimination. Toward that end, we constructed a GelCompar II database of DNA fingerprint patterns of ethidium bromide-stained EcoRI fragments of total LAB DNA separated by conventional agarose gel electrophoresis. We found that the total DNA patterns were strain-specific; 56/60 American Type Culture Collection strains of 33 species of LAB could be distinguished. Enterococcus faecium strains ATCC19434 and ATCC35667 had identical total DNA patterns and RiboPrints. Lactobacillus rhamnosus strains ATCC7469 and ATCC27773 also had identical total DNA patterns, but different RiboPrints. EcoRI RiboPrint patterns could distinguish only about 9/23 Lactobacillus plantarum strains and about 6/10 Lactobacillus buchneri strains, whereas all 33 strains could be distinguished by EcoRI total DNA patterns. Despite gel-to-gel variation, new DNA patterns can be readily grouped with existing patterns using GelCompar II. The database contains large homogenous clusters of L. plantarum, E. faecium, L. buchneri, Lactobacillus brevis and Pediococcus species that can be used for tentative taxonomic assignment. We routinely use the DNA fingerprint database to identify and characterize new strains, eliminate duplicate isolates and for quality control of inoculant product strains. The GelCompar II database has been in continuous use for 7 years and contains more than 3600 patterns representing approximately 700 unique patterns from over 300 gels and is the largest computerized DNA fingerprint database for LAB yet reported. PMID:14607400

Chan, Russell K; Wortman, Cora R; Smiley, Brenda K; Hendrick, Carol A

2003-12-01

52

GBshape: a genome browser database for DNA shape annotations  

PubMed Central

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. PMID:25326329

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J.; Parker, Stephen C.J.; Nuzhdin, Sergey V.; Tullius, Thomas D.; Rohs, Remo

2015-01-01

53

GBshape: a genome browser database for DNA shape annotations.  

PubMed

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. PMID:25326329

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J; Parker, Stephen C J; Nuzhdin, Sergey V; Tullius, Thomas D; Rohs, Remo

2015-01-01

54

DNA -- Intimate Information or Trash for Public Consumption?  

E-print Network

This essay discusses the increasingly popular police practice of covertly collecting DNA samples from people who inadvertently leave saliva, hair or other biological matter in public places. The essay contends that although the United States Supreme...

Wilson, Melanie D.

2008-01-01

55

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources  

PubMed Central

Background DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. Results We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Conclusion Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org. PMID:19958506

2009-01-01

56

PDA: a pipeline to explore and estimate polymorphism in large DNA databases  

PubMed Central

Polymorphism studies are one of the main research areas of this genomic era. To date, however, no available web server or software package has been designed to automate the process of exploring and estimating nucleotide polymorphism in large DNA databases. Here, we introduce a novel software, PDA, Pipeline Diversity Analysis, that automatically can (i) search for polymorphic sequences in large databases, and (ii) estimate their genetic diversity. PDA is a collection of modules, mainly written in Perl, which works sequentially as follows: unaligned sequence retrieved from a DNA database are automatically classified by organism and gene, and aligned using the ClustalW algorithm. Sequence sets are regrouped depending on their similarity scores. Main diversity parameters, including polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium and codon bias are estimated both for the full length of the sequences and for specific functional regions. Program output includes a database with all sequences and estimations, and HTML pages with summary statistics, the performed alignments and a histogram maker tool. PDA is an essential tool to explore polymorphism in large DNA databases for sequences from different genes, populations or species. It has already been successfully applied to create a secondary database. PDA is available on the web at http://pda.uab.es/. PMID:15215372

Casillas, Sňnia; Barbadilla, Antonio

2004-01-01

57

DNA patenting: implications for public health research.  

PubMed Central

I weigh the arguments for and against the patenting of functional DNA sequences including genes, and find the objections to be compelling. Is an outright ban on DNA patenting the right policy response? Not necessarily. Governments may wish to consider options ranging from patent law reforms to the creation of new rights. There are alternative ways to protect DNA sequences that industry may choose if DNA patenting is restricted or banned. Some of these alternatives may be more harmful than patents. Such unintended consequences of patent bans mean that we should think hard before concluding that prohibition is the only response to legitimate concerns about the appropriateness of patents in the field of human genomics. PMID:16710549

Dutfield, Graham

2006-01-01

58

The public Human Genome Project's DNA donors, Eric LanderSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Eric Lander DNAi Location: Genome>The Project>players>Public consortium The public's DNA donors Eric Lander, director of the Whitehead Institute Center for Genome Research, explains where the DNA donors for the first reference sequence came from.

2008-10-06

59

An assessment of whether SNPs will replace STRs in national DNA databases Joint considerations of the  

E-print Network

of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific as the preferred method of testing of forensic samples and database samples in the near to medium future and is not directly applicable to forensic use. This is because forensic scientists have to contend with small

60

Toward a mtDNA Locus-Specific Mutation Database Using the LOVD Platform  

PubMed Central

The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information. PMID:22581690

Elson, Joanna L.; Sweeney, Mary G.; Procaccio, Vincent; Yarham, John W.; Salas, Antonio; Kong, Qing-Peng; van der Westhuizen, Francois H.; Pitceathly, Robert D.S.; Thorburn, David R.; Lott, Marie T.; Wallace, Douglas C.; Taylor, Robert W.; McFarland, Robert

2015-01-01

61

DNAtraffic—a new database for systems biology of DNA dynamics during the cell life  

PubMed Central

DNAtraffic (http://dnatraffic.ibb.waw.pl/) is dedicated to be a unique comprehensive and richly annotated database of genome dynamics during the cell life. It contains extensive data on the nomenclature, ontology, structure and function of proteins related to the DNA integrity mechanisms such as chromatin remodeling, histone modifications, DNA repair and damage response from eight organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on the diseases related to the assembled human proteins. DNAtraffic is richly annotated in the systemic information on the nomenclature, chemistry and structure of DNA damage and their sources, including environmental agents or commonly used drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA network analysis. Database includes illustrations of pathways, damage, proteins and drugs. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines, it has to be extensively linked to numerous external data sources. Our database represents the result of the manual annotation work aimed at making the DNAtraffic much more useful for a wide range of systems biology applications. PMID:22110027

Kuchta, Krzysztof; Barszcz, Daniela; Grzesiuk, Elzbieta; Pomorski, Pawel; Krwawicz, Joanna

2012-01-01

62

Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases  

Microsoft Academic Search

Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard

D. H. Kaye

2006-01-01

63

An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections  

Technology Transfer Automated Retrieval System (TEKTRAN)

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated wi...

64

IRB and EDRC Release New Policy Governing Public Databases Date: February 22, 2013  

E-print Network

Director. The new policy identifies several well-known databases as meeting the definition of publicly in the Division of Epidemiology in MCW's Institute for Health and Society, with leadership from EDRC Director and Human Services definition of publicly available for exemption purposes. We are pleased to be able

65

Bibliometric analysis of Nigeria's social science and arts and humanities publications in Thomson Scientific databases  

Microsoft Academic Search

Purpose – This paper seeks to analyse publications on Nigeria indexed in Arts and Humanities Citation Index (AHCI) and Social Science Citation Index (SSCI) of Thomson Scientific databases respectively to understand the international perspective of aspects of research publication dynamics in both fields. Design\\/methodology\\/approach – Data covering the period 2002-2007 were collected from the SSCI and AHCI of the Web

Williams Nwagwu; Osakioduwa Egbon

2011-01-01

66

Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases  

SciTech Connect

Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard to these biobanks—the choice of loci to type for identifying individuals, the indefinite retention of DNA samples, and the use of the DNA samples or the identifying profiles for research purposes. It also considers the possible value of the databases for research into the genetics of human behavior and the ethics of using them for this purpose. It rejects the broad claim that such research is inherently unethical but proposes procedures for ensuring that the value of the proposed research justifies any psychosocial or other risks to the subjects of the research.

D.H. Kaye

2006-10-19

67

MisPred: a resource for identification of erroneous protein sequences in public databases.  

PubMed

Correct prediction of the structure of protein-coding genes of higher eukaryotes is still a difficult task; therefore, public databases are heavily contaminated with mispredicted sequences. The high rate of misprediction has serious consequences because it significantly affects the conclusions that may be drawn from genome-scale sequence analyses of eukaryotic genomes. Here we present the MisPred database and computational pipeline that provide efficient means for the identification of erroneous sequences in public databases. The MisPred database contains a collection of abnormal, incomplete and mispredicted protein sequences from 19 metazoan species identified as erroneous by MisPred quality control tools in the UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, NCBI/RefSeq and EnsEMBL databases. Major releases of the database are automatically generated and updated regularly. The database (http://www.mispred.com) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in a variety of formats. DATABASE URL: http://www.mispred.com. PMID:23864220

Nagy, Alinda; Patthy, László

2013-01-01

68

Big bad data: law, public health, and biomedical databases.  

PubMed

The accelerating adoption of electronic health record (EHR) systems will have far-reaching implications for public health research and surveillance, which in turn could lead to changes in public policy, statutes, and regulations. The public health benefits of EHR use can be significant. However, researchers and analysts who rely on EHR data must proceed with caution and understand the potential limitations of EHRs. Because of clinicians' workloads, poor user-interface design, and other factors, EHR data can be erroneous, miscoded, fragmented, and incomplete. In addition, public health findings can be tainted by the problems of selection bias, confounding bias, and measurement bias. These flaws may become all the more troubling and important in an era of electronic "big data," in which a massive amount of information is processed automatically, without human checks. Thus, we conclude the paper by outlining several regulatory and other interventions to address data analysis difficulties that could result in invalid conclusions and unsound public health policies. PMID:23590742

Hoffman, Sharona; Podgurski, Andy

2013-03-01

69

Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data.  

PubMed

We outline a paradigm for meta-microarray database creation and integration with clinical variables. We use as our implementation example a breast cancer database linking RNA expression measurements (by microarray) and clinical variables, such as survival metrics and tumor size. Such an endeavor involves integrating across different microarray datasets as well as clinical parameters. To this end, we created a data curation and processing pipeline, formal database ontology, and SQL schema to optimally query, analyze and visualize data from over 30 publicly available breast cancer microarray studies listed in the Gene Expression Omnibus (GEO). We demonstrate several pilot examples using this database. This methodology serves as a model for future meta-analyses of complex public clinical datasets, in particular those in the field of cancer. PMID:24303324

Planey, Catherine R; Butte, Atul J

2013-01-01

70

HUNT: launch of a full-length cDNA database from the Helix Research Institute.  

PubMed

The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project principally funded by the Japanese Ministry of International Trade and Industry, and the clones were sequenced in the governmental New Energy and Industrial Technology Development Organization (NEDO) Human cDNA Sequencing Project. The HUNT database contains an extensive amount of annotation from advanced analysis and represents an essential bioinformatics contribution towards understanding of the gene function. The HRI human cDNA clones were obtained from full-length enriched cDNA libraries constructed with the oligo-capping method and have resulted in novel full-length cDNA sequences. A large fraction has little similarity to any proteins of known function and to obtain clues about possible function we have developed original analysis procedures. Any putative function deduced here can be validated or refuted by complementary analysis results. The user can also extract information from specific categories like PROSITE patterns, PFAM domains, PSORT localization, transmembrane helices and clones with GENIUS structure assignments. The HUNT database can be accessed at http://www.hri.co.jp/HUNT. PMID:11125086

Yudate, H T; Suwa, M; Irie, R; Matsui, H; Nishikawa, T; Nakamura, Y; Yamaguchi, D; Peng, Z Z; Yamamoto, T; Nagai, K; Hayashi, K; Otsuki, T; Sugiyama, T; Ota, T; Suzuki, Y; Sugano, S; Isogai, T; Masuho, Y

2001-01-01

71

Geographical Analysis of Aneurysmal Subarachnoid Hemorrhage in Japan Utilizing Publically-Accessible DPC Database  

PubMed Central

Since the launch of the novel medical reimbursement system Diagnosis Procedure Combination (DPC) in 2003 in Japan, inpatient data has been accumulated over time as part of a Japanese governmental nationwide database. This is partially accessible by the public, and this study examined the adequacy of this database as epidemiological research material by extracting the data relating to aneurysmal subarachnoid hemorrhage (aSAH) with special attention given to the limitations that this involves. Datasets after 2010 are considered suitable for analysis because of the numbers of participating hospitals and the analysis term. Extracting the data by prefecture, those with a continuously high aSAH incidence were Aomori, Iwate, Akita, Yamagata, Kochi and Kumamoto Prefectures, and those with low aSAH incidence were Kanagawa, Shiga, Kyoto, Shimane and Ehime Prefectures. Although these obtained results are informative, a publically-accessible DPC database has several limitations. Some limitations have been resolved: the analyzed term each year is now 12-months and the number of participating hospitals seems to have stabilized around 1700. However, other limitations such as masking the numbers in each hospital reporting less than 10 patients still exist, so careful and critical interpretation is necessary in utilizing a publically-accessible DPC database. Considering the potential of this database as material for epidemiological research, future analysis of the entire DPC database by qualified researchers is desirable. PMID:25811480

Fukuhara, Toru

2015-01-01

72

Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases.  

PubMed

Inhibitors of DNA methyltransferase (DNMT) are attractive compounds not only as potential therapeutic agents for the treatment of cancer and other diseases, but also as research tools to investigate the role of DNMTs in epigenetic events. Recent advances in high-throughput screening (HTS) for epigenetic targets and the availability of the first crystallographic structure of human DNMT1 encourage the integration of research strategies to uncover and optimize the activity of DNMT inhibitors. Herein, we present a binding model of a novel small-molecule DNMT1 inhibitor obtained by HTS, recently released in a public database. The docking model is in agreement with key interactions previously identified for established inhibitors using extensive computational studies including molecular dynamics and structure-based pharmacophore modeling. Based on the chemical structure of the novel inhibitor, a sequential computational screening of five chemical databases was performed to identify candidate compounds for testing. Similarity searching followed by molecular docking of chemical databases such as approved drugs, natural products, a DNMT-focused library, and a general screening collection, identified at least 108 molecules with promising DNMT inhibitory activity. The chemical structures of all hit compounds are disclosed to encourage the research community working on epigenetics to test experimentally the enzymatic and demethylating activity in vivo. Five candidate hits are drugs approved for other indications and represent potential starting points of a drug repurposing strategy. PMID:23447100

Medina-Franco, José L; Yoo, Jakyung

2013-05-01

73

DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome.  

PubMed

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants ( https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5 ). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases. PMID:23720012

Savige, Judy; Ars, Elisabet; Cotton, Richard G H; Crockett, David; Dagher, Hayat; Deltas, Constantinos; Ding, Jie; Flinter, Frances; Pont-Kingdon, Genevieve; Smaoui, Nizar; Torra, Roser; Storey, Helen

2014-06-01

74

Use of DNA profiles for investigation using a simulated national DNA database: Part I. Partial SGM Plus profiles.  

PubMed

In traditional criminal investigation, uncertainties are often dealt with using a combination of common sense, practical considerations and experience, but rarely with tailored statistical models. For example, in some countries, in order to search for a given profile in the national DNA database, it must have allelic information for six or more of the ten SGM Plus loci for a simple trace. If the profile does not have this amount of information then it cannot be searched in the national DNA database (NDNAD). This requirement (of a result at six or more loci) is not based on a statistical approach, but rather on the feeling that six or more would be sufficient. A statistical approach, however, could be more rigorous and objective and would take into consideration factors such as the probability of adventitious matches relative to the actual database size and/or investigator's requirements in a sensible way. Therefore, this research was undertaken to establish scientific foundations pertaining to the use of partial SGM Plus loci profiles (or similar) for investigation. PMID:20457051

Hicks, T; Taroni, F; Curran, J; Buckleton, J; Ribaux, O; Castella, V

2010-07-01

75

Development and Evaluation of a Quality-Controlled Ribosomal Sequence Database for 16S Ribosomal DNA-Based Identification of Staphylococcus Species  

PubMed Central

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5? end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of ?98.7% similarity for a “distinct species,” a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMérieux, Marcy I'Etoile, France) and VITEK 2 (bioMérieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants. PMID:15528685

Becker, Karsten; Harmsen, Dag; Mellmann, Alexander; Meier, Christian; Schumann, Peter; Peters, Georg; von Eiff, Christof

2004-01-01

76

The Neutron Monitor database as a tool for space weather, education, and public outreach  

NASA Astrophysics Data System (ADS)

The Neutron Monitor database (NMDB) was created to make measurements from ground-based Neutron Monitors easily accessible. Data from more than 40 stations is available in the database and can be plotted via a webpage and downloaded as ASCII tables for further processing. Real-time applications, like the GLE Alert, can access the database directly. The NMDB project has also hosted training sessions and created extensive public outreach and training material that has been translated into 11 languages. This material is openly available on the NMDB website and is frequently used in highschool and university courses. While the availability of data from currently operating stations is nearing completion, the availability of historical data, especially no longer operating stations, is still limited. We are currently trying to fill these gaps. As a first step a project to make NMDB compatible with the database of relativistic solar particle events (GLEs) is starting this year.

Steigies, Christian T.; Klein, Karl-Ludwig; Bütikofer, Rolf

2014-05-01

77

Toward a public analysis database for LHC new physics searches using M ADA NALYSIS 5  

NASA Astrophysics Data System (ADS)

We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

Dumont, B.; Fuks, B.; Kraml, S.; Bein, S.; Chalons, G.; Conte, E.; Kulkarni, S.; Sengupta, D.; Wymant, C.

2015-02-01

78

Governing Software: Networks, Databases and Algorithmic Power in the Digital Governance of Public Education  

ERIC Educational Resources Information Center

This article examines the emergence of "digital governance" in public education in England. Drawing on and combining concepts from software studies, policy and political studies, it identifies some specific approaches to digital governance facilitated by network-based communications and database-driven information processing software…

Williamson, Ben

2015-01-01

79

HEDS - EPA DATABASE SYSTEM FOR PUBLIC ACCESS TO HUMAN EXPOSURE DATA  

EPA Science Inventory

Human Exposure Database System (HEDS) is an Internet-based system developed to provide public access to human-exposure-related data from studies conducted by EPA's National Exposure Research Laboratory (NERL). HEDS was designed to work with the EPA Office of Research and Devel...

80

STANDARDIZATION AND STRUCTURAL ANNOTATION OF PUBLIC TOXICITY DATABASES: IMPROVING SAR CAPABILITIES AND LINKAGE TO 'OMICS DATA  

EPA Science Inventory

Standardization and structural annotation of public toxicity databases: Improving SAR capabilities and linkage to 'omics data Ann M. Richard', ClarLynda Williams', Jamie Burch2 'Nat Health & Environ Res Lab, US EPA, RTP, NC 27711; 2EPA/NC Central Univ Student COOP Trainee...

81

Harp: a distributed query system for legacy public libraries and structured databases  

Microsoft Academic Search

The main purpose of a digital library is to facilitate users easy access to enormous amount of globally networked information. Typically, this information includes preexisting public library catalog data, digitized document collections, and other databases. In this article, we describe the distributed query system of a digital library prototype system known as HARP. In the HARP project, we have designed

Ee-Peng Lim; Ying Lu

1999-01-01

82

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations  

Microsoft Academic Search

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were

Peter Gill; Lindsey Foreman; John S Buckleton; Christopher M Triggs; Heather Allen

2003-01-01

83

Information Technologies in Public Health Management: A Database on Biocides to Improve Quality of Life  

PubMed Central

Background Biocides for prolonging the shelf life of a large variety of materials have been extensively used over the last decades. It has estimated that the worldwide biocide consumption to be about 12.4 billion dollars in 2011, and is expected to increase in 2012. As biocides are substances we get in contact with in our everyday lives, access to this type of information is of paramount importance in order to ensure an appropriate living environment. Consequently, a database where information may be quickly processed, sorted, and easily accessed, according to different search criteria, is the most desirable solution. The main aim of this work was to design and implement a relational database with complete information about biocides used in public health management to improve the quality of life. Methods: Design and implementation of a relational database for biocides, by using the software “phpMyAdmin”. Results: A database, which allows for an efficient collection, storage, and management of information including chemical properties and applications of a large quantity of biocides, as well as its adequate dissemination into the public health environment. Conclusion: The information contained in the database herein presented promotes an adequate use of biocides, by means of information technologies, which in consequence may help achieve important improvement in our quality of life. PMID:23113190

Roman, C; Scripcariu, L; Diaconescu, RM; Grigoriu, A

2012-01-01

84

Publicly Available Database : Improved Spectral Line Measurements In SDSS DR7 Galaxies  

NASA Astrophysics Data System (ADS)

We present a new database of absorption and emission line measurements based on the Sloan Digital Sky Survey 7th data release for the galaxies within a redshift of 0.2. Our work makes use of the publicly available penalized pixel-fitting(pPXF) and GANDALF codes, aiming to improve the existing measurements for stellar kinematics, the strength of various absorption-line features, and the flux and width of the emissions from different species of ionized gas. The absorption line strengths measured by SDSS pipeline are seriously contaminated by emission fill-in. We effectively separate emission lines from absorption lines. For instance, this work successfully extract [NI] doublet from Mgb and it leads to more realistic result of alpha enhancement on late-type galaxies compared to the previous database. Besides accurately measuring line strengths, the database provides new parameters that are indicative of line strength measurement quality. Users can build a subset of database optimal for their studies using specific cuts in the fitting quality parameters as well as empirical signal-to-noise. Applying these parameters, we found `hidden’ broad-line-region galaxies and they turned out to be Seyfert I nuclei that were not picked up as AGN by SDSS. The database is publicly available at http://gem.yonsei.ac.kr/ossy

Oh, Kyuseok; Sarzi, M.; Schawinski, K.; Yi, S. K.

2012-01-01

85

FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium  

Microsoft Academic Search

One of the greatest impediments to the study of Fusarium has been the incorrect and confused application of species names to toxigenic and pathogenic isolates, owing in large part to intrinsic limitations of morphological species recognition and its application. To address this problem, we have created FUSARIUM-ID v. 1.0, a publicly available database of partial translation elongation factor 1-alpha (TEF)

David M. Geiser; María del Mar Jiménez-Gasco; Seogchan Kang; Izabela Makalowska; Narayanan Veeraraghavan; Todd J. Ward; Ning Zhang; Gretchen A. Kuldau; Kerry O'donnell

2004-01-01

86

A large publicly accessible prototype audio database for music research. ISMIR  

E-print Network

This paper introduces Codaich, a large and diverse publicly accessible database of musical recordings for use in music information retrieval (MIR) research. The issues that must be dealt with when constructing such a database are discussed, as are ways of addressing these problems. It is suggested that copyright restrictions may be overcome by allowing users to make customized feature extraction queries rather than allowing direct access to recordings themselves. The jMusicMetaManager software is introduced as a tool for improving metadata associated with recordings by automatically detecting inconsistencies and redundancies.

Cory Mckay

2006-01-01

87

Constructing a robust protein-protein interaction network by integrating multiple public databases  

PubMed Central

Background Protein-protein interactions (PPIs) are a critical component for many underlying biological processes. A PPI network can provide insight into the mechanisms of these processes, as well as the relationships among different proteins and toxicants that are potentially involved in the processes. There are many PPI databases publicly available, each with a specific focus. The challenge is how to effectively combine their contents to generate a robust and biologically relevant PPI network. Methods In this study, seven public PPI databases, BioGRID, DIP, HPRD, IntAct, MINT, REACTOME, and SPIKE, were used to explore a powerful approach to combine multiple PPI databases for an integrated PPI network. We developed a novel method called k-votes to create seven different integrated networks by using values of k ranging from 1-7. Functional modules were mined by using SCAN, a Structural Clustering Algorithm for Networks. Overall module qualities were evaluated for each integrated network using the following statistical and biological measures: (1) modularity, (2) similarity-based modularity, (3) clustering score, and (4) enrichment. Results Each integrated human PPI network was constructed based on the number of votes (k) for a particular interaction from the committee of the original seven PPI databases. The performance of functional modules obtained by SCAN from each integrated network was evaluated. The optimal value for k was determined by the functional module analysis. Our results demonstrate that the k-votes method outperforms the traditional union approach in terms of both statistical significance and biological meaning. The best network is achieved at k=2, which is composed of interactions that are confirmed in at least two PPI databases. In contrast, the traditional union approach yields an integrated network that consists of all interactions of seven PPI databases, which might be subject to high false positives. Conclusions We determined that the k-votes method for constructing a robust PPI network by integrating multiple public databases outperforms previously reported approaches and that a value of k=2 provides the best results. The developed strategies for combining databases show promise in the advancement of network construction and modeling. PMID:22165958

2011-01-01

88

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.  

PubMed

REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email. PMID:25378308

Roberts, Richard J; Vincze, Tamas; Posfai, Janos; Macelis, Dana

2015-01-01

89

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes  

PubMed Central

REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email. PMID:25378308

Roberts, Richard J.; Vincze, Tamas; Posfai, Janos; Macelis, Dana

2015-01-01

90

Local mitochondrial DNA haplotype databases needed for domestic dog populations that have experienced founder effect.  

PubMed

Biological material from pets is often collected as evidence from crime scenes. Due to sample type and quality, mitochondrial DNA (mtDNA) is frequently evaluated to identify the potential contributor. MtDNA has a lower discriminatory power than nuclear DNA with multiple individuals in a population potentially carrying the same mtDNA sequence, or haplotype. The frequency distribution of mtDNA haplotypes in a population must be known in order to determine the evidentiary value of a match between crime scene evidence and the potential contributor of the biological material. This is especially important in geographic areas that include remote and/or isolated populations where founder effect may have lead to a decrease in genetic diversity and a non-random distribution of haplotypes relative to the population at large. Here we compared the haplotype diversity in dogs from the noncontiguous states of Alaska and Hawaii relative to the contiguous United States (US). We report a greater proportion of dogs carrying an A haplotype in Alaska relative to any other US population. Significant variation in the distribution of haplotype frequencies was discovered when comparing the haplotype diversity of dogs in Hawaii to that of the continental US. Each of these regions exhibits reduced genetic diversity relative to the contiguous US, likely due to founder effect. We recommend that specific databases be created to accurately represent the mitochondrial haplotype diversity in these remote areas. Furthermore, our work demonstrates the importance of local surveys for populations that may have experienced found effect. PMID:25612881

Spadaro, Amanda; Ream, Kelsey; Braham, Caitlyn; Webb, Kristen M

2015-03-01

91

A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database  

PubMed Central

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-01-01

92

Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds  

PubMed Central

Background Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets. Results Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate standardised comparisons typically reduced source counts by between 5% and 30%. The pair-wise overlaps between 23 databases and subsets were determined, as well as changes between 2006 and 2008. While all compound sets have increased, PubChem has doubled to 14.2 million. The 2008 comparison matrix shows not only overlap but also unique content across all sources. Many of the detailed differences could be attributed to individual strategies for data selection and extraction. While there was a big increase in patent-derived structures entering PubChem since 2006, GVKBIO contains over 0.8 million unique structures from this source. Venn diagrams showed extensive overlap between compounds extracted by independent expert curation from journals by GVKBIO, WOMBAT (both commercial) and BindingDB (public) but each included unique content. In contrast, the approved drug collections from GVKBIO, MDDR (commercial) and DrugBank (public) showed surprisingly low overlap. Aggregating all commercial sources established that while 1 million compounds overlapped with PubChem 1.2 million did not. Conclusion On the basis of chemical structure content per se public sources have covered an increasing proportion of commercial databases over the last two years. However, commercial products included in this study provide links between compounds and information from patents and journals at a larger scale than current public efforts. They also continue to capture a significant proportion of unique content. Our results thus demonstrate not only an encouraging overall expansion of data-supported bioactive chemical space but also that both commercial and public sources are complementary for its exploration. PMID:20298516

2009-01-01

93

A spatial national health facility database for public health sector planning in Kenya in 2008  

PubMed Central

Background Efforts to tackle the enormous burden of ill-health in low-income countries are hampered by weak health information infrastructures that do not support appropriate planning and resource allocation. For health information systems to function well, a reliable inventory of health service providers is critical. The spatial referencing of service providers to allow their representation in a geographic information system is vital if the full planning potential of such data is to be realized. Methods A disparate series of contemporary lists of health service providers were used to update a public health facility database of Kenya last compiled in 2003. These new lists were derived primarily through the national distribution of antimalarial and antiretroviral commodities since 2006. A combination of methods, including global positioning systems, was used to map service providers. These spatially-referenced data were combined with high-resolution population maps to analyze disparity in geographic access to public health care. Findings The updated 2008 database contained 5,334 public health facilities (67% ministry of health; 28% mission and nongovernmental organizations; 2% local authorities; and 3% employers and other ministries). This represented an overall increase of 1,862 facilities compared to 2003. Most of the additional facilities belonged to the ministry of health (79%) and the majority were dispensaries (91%). 93% of the health facilities were spatially referenced, 38% using global positioning systems compared to 21% in 2003. 89% of the population was within 5 km Euclidean distance to a public health facility in 2008 compared to 71% in 2003. Over 80% of the population outside 5 km of public health service providers was in the sparsely settled pastoralist areas of the country. Conclusion We have shown that, with concerted effort, a relatively complete inventory of mapped health services is possible with enormous potential for improving planning. Expansion in public health care in Kenya has resulted in significant increases in geographic access although several areas of the country need further improvements. This information is key to future planning and with this paper we have released the digital spatial database in the public domain to assist the Kenyan Government and its partners in the health sector. PMID:19267903

Noor, Abdisalan M; Alegana, Victor A; Gething, Peter W; Snow, Robert W

2009-01-01

94

The public sequencing process, John SulstonSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: John Sulston DNAi Location:Genome>The project>players>Public The public sequencing process Nobel Laureate John Sulston, a key figure in the UK sequencing effort, talks about breaking DNA apart so that the sequence can be reassembled.

2008-10-06

95

DNA perfume and improving public knowledge, Francis CollinsSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Francis Collins DNAi Location:Timeline>1990s I arrived here April the 4th, 1993, an auspicious day because that very day I, as I opened the newspaper I realized that that was probably going to be remembered in the annals of DNA, not because of me, because that didn't seem like that was going to be so significant, but because that was the day that DNA perfume was issued, all kinds of advertising all over the place about, go out and buy this perfume. And it was a bit jarring because the perfume bottle was in the shape of a helix but it was actually a triple helix, making it very clear we had an educational challenge as well as a scientific challenge if this project was ever going to achieve the public benefit that we all hoped for.

2008-03-26

96

First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification  

PubMed Central

Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. Description We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Conclusion Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading to increased tomato productivity in India as well as other parts of the world. In era of IPR the new variety can be identified based on allelic variation among varieties supplementing DUS test and product traceability.

2013-01-01

97

Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

Dogget, N.; Myers, G. [Los Alamos National Lab., NM (United States); Wills, C.J. [Univ. of California, San Diego, CA (United States)

1998-12-01

98

76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Public Use Database Incorporating High-Cost Single-Family Securitized Loan Data Fields...make public certain data related to high-cost single-family loans purchased and securitized...to include data fields for the high-cost single-family securitized loans...

2011-09-28

99

A Two-locus DNA Sequence Database for Typing Plant and Human Pathogens Within the Fusarium oxysporum Species Complex  

Technology Transfer Automated Retrieval System (TEKTRAN)

We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex ...

100

Publicly available database for spectral line measurements of SDSS DR7 galaxies  

NASA Astrophysics Data System (ADS)

We present a new database of absorption and emission-line measurements based on the Sloan Digital Sky Survey (SDSS) 7th data release of galaxies within a redshift of 0.2. Using the publicly available penalized pixel-fitting (pPXF) and gas and absorption line fitting (gandalf) codes, our work improve the existing measurements for stellar kinematics, the strength of various absorption line features, and the flux and width of the emissions from different species of ionised gas. Most notable of our work is that, we provide quality of the fit to assess reliability of the measurements. The quality assessment can be highly effective for finding new classes of objects. For example, based on the quality assessment around the Ha and [NII] nebular lines, we found approximately 1% of the SDSS spectra which classified as galaxies by the SDSS pipeline are in fact type I Seyfert AGN. This paper presents a summary of the recent paper, Oh et al.(2011). The database is publicly available at http://gem.yonsei.ac.kr/ossy/.

Oh, Kyuseok; Sarzi, Marc; Schawinski, Kevin; Yi, Sukyoung K.

2012-08-01

101

Public Perceptions and Expectations of the Forensic Use of DNA: Results of a Preliminary Study  

ERIC Educational Resources Information Center

The forensic use of Deoxyribonucleic Acid (DNA) is demonstrating significant success as a crime-solving tool. However, numerous concerns have been raised regarding the potential for DNA use to contravene cultural, ethical, and legal codes. In this article the expectations and level of knowledge of the New Zealand public of the DNA data-bank and…

Curtis, Cate

2009-01-01

102

DNA banking and DNA databanking: Legal, ethical, and public policy issues. Progress report, [April 1, 1993--March 31, 1994  

SciTech Connect

The purpose of the grant was to provide support to enable us to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus has both a research and analysis component and a public education component. This report outlines the work completed since the inception of the project and describes the activities still in progress.

Reilly, P.R.; McEwen, J.E.; Small, D.

1994-02-18

103

Covariation of the Incidence of Type 1 Diabetes with Country Characteristics Available in Public Databases  

PubMed Central

Background The incidence of Type 1 Diabetes (T1D) in children varies dramatically between countries. Part of the explanation must be sought in environmental factors. Increasingly, public databases provide information on country-to-country environmental differences. Methods Information on the incidence of T1D and country characteristics were searched for in the 194 World Health Organization (WHO) member countries. T1D incidence was extracted from a systematic literature review of all papers published between 1975 and 2014, including the 2013 update from the International Diabetes Federation. The information on country characteristics was searched in public databases. We considered all indicators with a plausible relation with T1D and those previously reported as correlated with T1D, and for which there was less than 5% missing values. This yielded 77 indicators. Four domains were explored: Climate and environment, Demography, Economy, and Health Conditions. Bonferroni correction to correct false discovery rate (FDR) was used in bivariate analyses. Stepwise multiple regressions, served to identify independent predictors of the geographical variation of T1D. Findings T1D incidence was estimated for 80 WHO countries. Forty-one significant correlations between T1D and the selected indicators were found. Stepwise Multiple Linear Regressions performed in the four explored domains indicated that the percentages of variance explained by the indicators were respectively 35% for Climate and environment, 33% for Demography, 45% for Economy, and 46% for Health conditions, and 51% in the Final model, where all variables selected by domain were considered. Significant environmental predictors of the country-to-country variation of T1D incidence included UV radiation, number of mobile cellular subscriptions in the country, health expenditure per capita, hepatitis B immunization and mean body mass index (BMI). Conclusions The increasing availability of public databases providing information in all global environmental domains should allow new analyses to identify further geographical, behavioral, social and economic factors, or indicators that point to latent causal factors of T1D. PMID:25706995

Diaz-Valencia, Paula Andrea; Bougnčres, Pierre; Valleron, Alain-Jacques

2015-01-01

104

Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): a database of permitted public-supply wells, surface-water intakes, and systems in the United States  

USGS Publications Warehouse

The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

Price, Curtis V.; Maupin, Molly A.

2014-01-01

105

Kingston Frontenac Public Library's Online Database Collection Copied from the A-to-Z Database List; Updated July 14, 2014  

E-print Network

of complementary, holistic and integrated approaches to health care and wellness. It offers full-text articles List; Updated July 14, 2014 Alt Health Watch This database focuses on the many perspectives their family history. AudioBookCloud Formerly known as TumbleTalkingBooks, this resources allows you to listen

Abolmaesumi, Purang

106

MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data  

PubMed Central

DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies. PMID:25294826

Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing; Zhang, Zhang

2015-01-01

107

Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.  

PubMed

The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We discuss the scientific basis of the familial search approach, other DNA-based methods for eliminating individuals from the candidate lists generated by these NDNAD searches, the value of filtering these lists by age, ethnic appearance and geography and the governance required by the NDNAD Strategy Board when a police force commissions a familial search. We present the FSS data in relation to the utility of the familial searching service and demonstrate the power of the technique by reference to casework examples. We comment on the uptake of familial searching of DNA databases in the USA, the Netherlands, Australia, and New Zealand. Finally, following the adverse ruling by the European Court of Human Rights against the UK in regard to the S & Marper cases and the consequent introduction of the Protection of Freedoms Act (2012), we discuss the impact that changes to regulations concerning the storage of DNA samples will have on the continuing provision of familial searching of the National DNA Database in England and Wales. PMID:24315582

Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

2014-01-01

108

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT  

EPA Science Inventory

Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development Many sources of public toxicity data are not currently linked to chemical structure, are not ...

109

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data  

SciTech Connect

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easy access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.

Starr, D. L. (Dan L.); Wozniak, P. R. (Przemyslaw R.); Vestrand, W. T. (W. Thomas)

2002-01-01

110

Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.  

PubMed

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3' sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids. PMID:14962987

Rise, Matthew L; von Schalburg, Kristian R; Brown, Gordon D; Mawer, Melanie A; Devlin, Robert H; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A Ross; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A; Nelson, Colleen; Jones, Simon R M; Smailus, Duane E; Jones, Steven J M; Schein, Jacqueline E; Marra, Marco A; Butterfield, Yaron S N; Stott, Jeff M; Ng, Siemon H S; Davidson, William S; Koop, Ben F

2004-03-01

111

Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)  

SciTech Connect

Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals.

Fostel, Jennifer M. [Global Health Sector, SRA International, Inc., LLC, Durham, North Carolina (United States)], E-mail: Fostel@niehs.nih.gov

2008-11-15

112

Potential translational targets revealed by linking mouse grooming behavioral phenotypes to gene expression using public databases  

PubMed Central

Rodent self-grooming is an important, evolutionarily conserved behavior, highly sensitive to pharmacological and genetic manipulations. Mice with aberrant grooming phenotypes are currently used to model various human disorders. Therefore, it is critical to understand the biology of grooming behavior, and to assess its translational validity to humans. The present in-silico study used publicly available gene expression and behavioral data obtained from several inbred mouse strains in the open-field, light-dark box, elevated plus- and elevated zero-maze tests. As grooming duration differed between strains, our analysis revealed several candidate genes with significant correlations between gene expression in the brain and grooming duration. The Allen Brain Atlas, STRING, GoMiner and Mouse Genome Informatics databases were used to functionally map and analyze these candidate mouse genes against their human orthologs, assessing the strain ranking of their expression and the regional distribution of expression in the mouse brain. This allowed us to identify an interconnected network of candidate genes (which have expression levels that correlate with grooming behavior), display altered patterns of expression in key brain areas related to grooming, and underlie important functions in the brain. Collectively, our results demonstrate the utility of large-scale, high-throughput data-mining and in-silico modeling for linking genomic and behavioral data, as well as their potential to identify novel neural targets for complex neurobehavioral phenotypes, including grooming. PMID:23123364

Roth, Andrew; Kyzar, Evan; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; O’Leary, Timothy P.; Tabakoff, Boris; Brown, Richard E.; Kalueff, Allan V.

2014-01-01

113

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools  

Microsoft Academic Search

Background: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here. Results: MAGIC-SPP is a DNA sequence

Chun Liang; Feng Sun; Haiming Wang; Junfeng Qu; Robert M. Freeman Jr; Lee H. Pratt; Marie-michčle Cordonnier-pratt

2006-01-01

114

GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions.  

PubMed

Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch (http://www.GABI-Kat.de) is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently, the database contains >108,000 mapped FSTs from approximately 64,000 lines which cover 64% of all annotated A.thaliana protein-coding genes. The web interface allows searching for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests. About 3500 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles. PMID:17062622

Li, Yong; Rosso, Mario G; Viehoever, Prisca; Weisshaar, Bernd

2007-01-01

115

A two-locus DNA sequence database for identifying host-specific pathogens and phylogenetic diversity within the Fusarium oxysporum species complex  

Technology Transfer Automated Retrieval System (TEKTRAN)

An electronically portable two-locus DNA sequence database, comprising partial sequences of the translation elongation factor gene (EF-1a, 634 bp alignment) and nearly complete sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA, 2220 bp alignment) for 850 isolates spanning the phy...

116

A Human Mitochondrial Genome Database  

NSDL National Science Digital Library

The Center for Molecular Medicine at Emory University maintains this human mitochondrial genome database, which offers information on Mitochondrial DNA Function Locations and Polypeptide Assignments as well as the relevant publication references. The database is initially searchable by gene, disease, and enzyme. Users can then refine their search by function, polymorphisms, or references (author, title, journal, year, or keyword). Users can also search the references directly via an Advanced Search. An additional resource at the site is a reference guide to mitomap tables featuring searchable (by keyword) information on specific mitochondrial DNA function locations and references. An opportunity to add publications to this database is available, if users find that pertinent papers have not been cited.

Brown, M.D.

1996-01-01

117

Minors or suspects? A discussion of the legal and ethical issues surrounding the indefinite storage of DNA collected from children aged 10-18 years on the National DNA Database in England and Wales.  

PubMed

There are currently over 250,000 children between the ages of 10 and 18 years who have their genetic information stored on the National DNA Database. This paper explores the legal and ethical issues surrounding this controversial subject, with particular focus on juvenile capacity and the potential results of criminalizing young children and adolescents. The implications of the adverse legal judgement of the European Court of Human Rights in S and Marper v UK (2008) and the violation of Article 8 of the Convention are discussed. The authors have considered the requirement to balance the rights of the individual, particularly those of minors, against the need to protect the public and have compared the position in Scotland to that of the rest of the UK. The authors conclude that a more ethically acceptable alternative could be the creation of a separate forensic database for children aged 10-18 years, set up to safeguard the interests of those who have not been convicted of any crime. PMID:22941519

Mansel, Charlotte; Davies, Sharon

2012-10-01

118

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome  

PubMed Central

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A.

2015-01-01

119

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.  

PubMed

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A

2015-01-01

120

CMD: A Cotton Microsatellite Database Resource for Gossypium Genomics  

Technology Transfer Automated Retrieval System (TEKTRAN)

The Cotton Microsatellite Database (CMD) is a curated and integrated web-based database providing centralized access to all publicly available cotton microsatellite markers (SSRs) (http://www.cottonssr.org). At present it contains DNA sequence, SSR marker, mapping and similarity data for nine cotton...

121

Development of Energy Consumption Database Management System of Existing Large Public Buildings  

E-print Network

The statistic data of energy consumption are the base of analyzing energy consumption. The scientific management method of energy consumption data and the development of database management system plays an important role in building energy...

Li, Y.; Zhang, J.; Sun, D.

2006-01-01

122

Contamination of cDNA libraries and expressed sequence-tags databases  

SciTech Connect

Partially sequenced cDNAs, or expressed sequence tags (ESTs), are claimed to represent an efficient strategy for characterizing an organism`s genes. By necessity, these sequences are incompletely characterized, and examples of contamination of cDNA libraries with sequences from other species have been described. It has been suggested that a Human T-cell cDNA library (Clontech HL1963g) is contaminated by sequences from yeast (Saccharomyces cerevisiae) and an unknown bacterium. We are characterizing human ESTs that represent new members of the ATP-binding cassette transporter super-family. In examining human ESTs generated from the T-cell library, we have encountered one gene that was in fact a yeast sequence (Genbank Z15214 = SSH2 locus) and several genes that do not hybridize to human DNA or RNA. PCR primers from these sequences failed to amplify a product from human, yeast, or Escherichia coli DNA but did produce a product from a Clontech kidney cDNA library (HL1123a). To determine the source of the contamination, we amplified a conserved segment of the 16S rDNA (following a suggestion from Dr. C. Savakis) from the kidney library. The sequence of this product was nearly identical to that of the bacterium Leuconostoc lactis (300 of 304 bp). Leuconostoc species are commonly found in dairy products, fruits, vegetables, and wine and are nonpathogenic to humans. 6 refs., 1 fig.

Dean, M.; Allikmets, R. [Frederick Cancer Research and Development Center, MD (United States)

1995-11-01

123

The MOSART Database: Linking the SART CORS Clinical Database to the Population-Based Massachusetts PELL Reproductive Public Health Data System  

PubMed Central

Although Assisted Reproductive Technology (ART) births make up 1.6 % of births in the US, the impact of ART on subsequent infant and maternal health is not well understood. Clinical ART treatment records linked to population data would be a powerful tool to study long term outcomes among those treated or not by ART. This paper describes the development of a database intended to accomplish this task. We constructed the Massachusetts Outcomes Study of Assisted Reproductive Technology (MOSART) database by linking the Society of Assisted Reproductive Technologies Clinical Outcomes Reporting System (SART CORS) and the Massachusetts (MA) Pregnancy to Early Life Longitudinal (PELL) data systems for children born to MA resident women at MA hospitals between July 2004 and December 2008. PELL data representing 282,971 individual women and their 334,152 deliveries and 342,035 total births were linked with 48,578 cycles of ART treatment in SART CORS delivered to MA residents or women receiving treatment in MA clinics, representing 18,439 eligible women of whom 9,326 had 10,138 deliveries in this time period. A deterministic five phase linkage algorithm methodology was employed. Linkage results, accuracy, and concordance analyses were examined. We linked 9,092 (89.7 %) SART CORS outcome records to PELL delivery records overall, including 95.0 % among known MA residents treated in MA clinics; 70.8 % with full exact matches. There were minimal differences between matched and unmatched delivery records, except for unknown residency and out-of-state ART site. There was very low concordance of reported use of ART treatment between SART CORS and PELL (birth certificate) data. A total of 3.4 % of MA children (11,729) were identified from ART assisted pregnancies (6,556 singletons; 5,173 multiples). The MOSART linked database provides a strong basis for further longitudinal ART outcomes studies and supports the continued development of potentially powerful linked clinical-public health databases. PMID:24623195

Hoang, Lan; Stern, Judy E.; Diop, Hafsatou; Belanoff, Candice; Declercq, Eugene

2015-01-01

124

A brief history of the formation of DNA databases in forensic science within Europe  

Microsoft Academic Search

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which

Peter D. Martin; Hermann Schmitter; Peter M. Schneider

2001-01-01

125

Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing?  

PubMed Central

In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context. PMID:24054029

Eduardoff, Mayra; Huber, Gabriela; Bayer, Birgit; Schmid, Dagmar; Anslinger, Katja; Göbel, Tanja; Zimmermann, Bettina; Schneider, Peter M.; Röck, Alexander W.; Parson, Walther

2013-01-01

126

Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database  

PubMed Central

To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, ?-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles. PMID:19916789

Lindsey, Rebecca L.; Rondeau, Gaelle; Porwollik, Steffen; Long, Fred; McClelland, Michael; Jackson, Charlene R.; Englen, Mark D.; Meinersmann, Richard J.; Berrang, Mark E.; Davis, Johnnie A.; Barrett, John B.; Turpin, Jennifer B.; Thitaram, Sutawee N.; Fedorka-Cray, Paula J.

2010-01-01

127

PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples.  

PubMed

PreDREM is a database of DNA regulatory motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples. It contains 845-1325 predicted motifs in each sample, which result in a total of 2684 non-redundant motifs. In comparison with seven large collections of known motifs, more than 84% of the 2684 predicted motifs are similar to the known motifs, and 54-76% of the known motifs are similar to the predicted motifs. PreDREM also stores 43 663-20 13 288 motif modules in each sample, which provide the cofactor motifs of each predicted motif. Compared with motifs of known interacting transcription factor (TF) pairs in eight resources, on average, 84% of motif pairs corresponding to known interacting TF pairs are included in the predicted motif modules. Through its web interface, PreDREM allows users to browse motif information by tissues, datasets, individual non-redundant motifs, etc. Users can also search motifs, motif modules, instances of motifs and motif modules in given genomic regions, tissue or cell types a motif occurs, etc. PreDREM thus provides a useful resource for the understanding of cell- and tissue-specific gene regulation in the human genome. Database URL: http://server.cs.ucf.edu/predrem/. PMID:25725063

Zheng, Yiyu; Li, Xiaoman; Hu, Haiyan

2015-01-01

128

PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples  

PubMed Central

PreDREM is a database of DNA regulatory motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples. It contains 845–1325 predicted motifs in each sample, which result in a total of 2684 non-redundant motifs. In comparison with seven large collections of known motifs, more than 84% of the 2684 predicted motifs are similar to the known motifs, and 54–76% of the known motifs are similar to the predicted motifs. PreDREM also stores 43 663–20 13 288 motif modules in each sample, which provide the cofactor motifs of each predicted motif. Compared with motifs of known interacting transcription factor (TF) pairs in eight resources, on average, 84% of motif pairs corresponding to known interacting TF pairs are included in the predicted motif modules. Through its web interface, PreDREM allows users to browse motif information by tissues, datasets, individual non-redundant motifs, etc. Users can also search motifs, motif modules, instances of motifs and motif modules in given genomic regions, tissue or cell types a motif occurs, etc. PreDREM thus provides a useful resource for the understanding of cell- and tissue-specific gene regulation in the human genome. Database URL: http://server.cs.ucf.edu/predrem/. PMID:25725063

Zheng, Yiyu; Li, Xiaoman; Hu, Haiyan

2015-01-01

129

DNA DNA DNA (d)DNA DNA DNA  

E-print Network

DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

Hagiya, Masami

130

Molecular solutions of the RSA public-key cryptosystem on a DNA-based computer  

Microsoft Academic Search

The RSA public-key cryptosystem is an algorithm that converts a plain-text to its corresponding cipher-text, and then converts\\u000a the cipher-text back into its corresponding plain-text. In this article, we propose five DNA-based algorithms—parallel adder,\\u000a parallel subtractor, parallel multiplier, parallel comparator, and parallel modular arithmetic—that construct molecular solutions\\u000a for any (plain-text, cipher-text) pair for the RSA public-key cryptosystem. Furthermore, we demonstrate

Weng-Long Chang; Kawuu Weicheng Lin; Ju-Chin Chen; Chih-Chiang Wang; Lai Chin Lu; Minyi Guo

131

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species  

PubMed Central

Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php. PMID:24948109

2014-01-01

132

Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba.  

PubMed

Species of Acanthamoeba have been traditionally described using morphology (primarily cyst structure), or cytology of nuclear division (used by Pussard and Pons, 1977). Twenty-plus putative species were proposed based on such criteria. Morphology, however, is often plastic, dependent upon culture conditions. DNA sequences of the nuclear small subunit (18S) rRNA that can be used for the study of the phylogeny of Acanthamoeba have increased from a single sequence in 1986 to more than 1800 in 2013. Some of the patterns of the sequence data for Acanthamoeba are reviewed, and some of the insights that this data illuminates are illustrated. In particular, the data suggest the existence of 20 or more genotypic types, a number not dissimilar to the number of named species of Acanthamoeba. However, molecular studies make clear that the relationship between phylogenetic relatedness and species names as we know them for Acanthamoeba is tenuous at best. PMID:24999094

Fuerst, Paul A

2014-11-01

133

Rationale and Uses of a Public HIV Drug-Resistance Database  

PubMed Central

Knowledge regarding the drug resistance of human immunodeficiency virus (HIV) is critical for surveillance of drug resistance, development of antiretroviral drugs, and management of infections with drug-resistant viruses. Such knowledge is derived from studies that correlate genetic variation in the targets of therapy with the antiretroviral treatments received by persons from whom the variant was obtained (genotype-treatment), with drug-susceptibility data on genetic variants (genotype-phenotype), and with virological and clinical response to a new treatment regimen (genotype-outcome). An HIV drug-resistance database is required to represent, store, and analyze the diverse forms of data underlying our knowledge of drug resistance and to make these data available to the broad community of researchers studying drug resistance in HIV and clinicians using HIV drug-resistance tests. Such genotype-treatment, genotype-phenotype, and genotype-outcome correlations are contained in the Stanford HIV RT and Protease Sequence Database and have specific usefulness. PMID:16921473

Shafer, Robert W.

2008-01-01

134

Seabird databases and the new paradigm for scientific publication and attribution  

USGS Publications Warehouse

For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

Hatch, Scott A.

2010-01-01

135

'Ancient' DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database.  

PubMed Central

Recent work on the diapausing egg banks of zooplankton, such as Daphnia (Crustacea: Anomopoda), indicates that these eggs can remain viable for decades while, theoretically, DNA can remain intact for even longer periods (i.e. centuries or millennia). We isolated diapausing eggs of Daphnia from a 30 m long sediment core taken from a hypereutrophic, northern German lake (Belauer See), with some eggs found in dated core material as old as 4500 years. Using microsatellite markers, we analysed the genetic structure of the resting eggs dated as old as ca. 200 years, and found that, although levels of heterozygosity remained remarkably stable, significant genetic differentiation (Nei's D = 0.36; F(ST) = 0.15) between recent and 'ancient' resting eggs (including allele frequency shifts and private alleles) was detected. These shifts represent either species-level changes in this complex (i.e. species-specific characters of ephippia are not always robust), or intraspecific shifts in genetic variation, or a combination of both. This study demonstrates that the egg banks of aquatic zooplankton can serve as repositories of both genetic (intrapopulational) and ecological (interspecific) information. The use of molecular markers, such as microsatellites, on diapausing egg/seed banks may open new avenues of enquiry related to tracking the long-term genetic (and/or species) shifts that are associated with long-term environmental changes. PMID:11839197

Limburg, Petra A; Weider, Lawrence J

2002-01-01

136

A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.  

PubMed

MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA-mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs-above what could be observed in randomly generated gene lists-suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net. PMID:18812437

Creighton, Chad J; Nagaraja, Ankur K; Hanash, Samir M; Matzuk, Martin M; Gunaratne, Preethi H

2008-11-01

137

ENVIRONMENTAL RESIDUE EFFECTS DATABASE (ERED)  

EPA Science Inventory

US Army Corps of Engineers public web site for the "Environmental Residue Effects Database", a searchable database of adverse biological effects associated with tissue concentrations of various contaminants....

138

DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database.  

PubMed

Caves represent a unique environment in which to study subsurface geomicrobial interactions and processes. One of the primary techniques used to study such geologic samples is molecular phylogenetic analysis, but this technique is hampered by low microbial biomass and calcium in the host rock, often leading to poor and irreproducible DNA extraction. We describe an improved protocol to recover extremely low amounts of DNA from calcium-rich geologic samples. This protocol relies on the use of the synthetic DNA molecule poly-dIdC, to act both as blocking agent and carrier molecule to increase the yield of DNA, and dialysis to remove calcium inhibitors of PCR amplification. Further, we demonstrate that many traditionally used laboratory substrates contain microbial DNA that can be amplified through the polymerase chain reaction (PCR) and contaminate molecular phylogenetic profiles. While the number of potential contaminants can be minimized, it cannot be eliminated from extraction techniques. We have therefore established the low-biomass contaminant (LBC) database, which contains the 16S rRNA gene sequences of species that have been identified as common laboratory contaminants. These identified contaminants provide a reference database to allow investigators to critically evaluate certain species identified within their phylogenetic profile when examining such low-biomass environments. PMID:16305811

Barton, H A; Taylor, N M; Lubbers, B R; Pemberton, A C

2006-07-01

139

Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian  

PubMed Central

Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

2008-01-01

140

The Mission Accessible Near-Earth Object Survey Public Database Development Effort  

NASA Astrophysics Data System (ADS)

The Mission Accessible Near-Earth Object Survey (MANOS) began in August 2013 as a multi-year physical characterization survey that was awarded large survey status by NOAO. MANOS will target several hundred mission-accessible NEOs across visible and near-infrared wavelengths, ultimately providing a comprehensive catalog of physical properties (astrometry, light curves, spectra). The MANOS project will provide a resource that not only helps to manage our survey in a fully transparent, publicly accessible forum, but will also help to coordinate minor planet characterization efforts and target prioritization across multiple research groups. Working towards that goal, we are developing a portal for rapid, up to date, public dissemination of our data. Migrating the Lowell Astorb dataset to a SQL framework is a major step towards the modernization of the system and will make capable up-to-date deployment of data. This will further allow us to develop utilities of various complexity, such as a deltaV calculator, minor planet finder charts, and sophisticated ephemeri generation functions. We present the state of this effort and a preliminary timeline for functionality.

Burt, Brian; Moskovitz, Nicholas; Putnam, Lowell

2014-11-01

141

Creating a data exchange strategy for radiotherapy research: towards federated databases and anonymised public datasets.  

PubMed

Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within "Big Data". Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology. PMID:25458128

Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

2014-12-01

142

Microgravity Database  

NSDL National Science Digital Library

The European Space Agencies (ESA) Microgravity Database "gives scientists access to information regarding all experiments carried out on ESA and NASA missions by European scientists since the 1960s." Users choose from a physical or life sciences query form, then can search by experiment and investigators, mission and facility, publications and source, and more. Results provide the mission name, data, payload, research subject, publication information, an abstract, and any other available facts or related links. A very intuitive and well designed database, visitors should appreciate its unique and extensive content.

143

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum.  

PubMed

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11. 149.55/). Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, we have produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. PMID:11125052

Watanabe, J; Sasaki, M; Suzuki, Y; Sugano, S

2001-01-01

144

Lung Image Databases-2  

Cancer.gov

Lung Image Database Consortium’s Normalized Relational Database • De-identified (anonymized) CT datasets • Publicly accessible • Web search tools • Cases from search results can be downloaded – ftp or DICOM De-identified CT datasets Digital Imaging and

145

Comparing subjective image quality measurement methods for the creation of public databases  

NASA Astrophysics Data System (ADS)

The Single Stimulus (SS) method is often chosen to collect subjective data testing no-reference objective metrics, as it is straightforward to implement and well standardized. At the same time, it exhibits some drawbacks; spread between different assessors is relatively large, and the measured ratings depend on the quality range spanned by the test samples, hence the results from different experiments cannot easily be merged . The Quality Ruler (QR) method has been proposed to overcome these inconveniences. This paper compares the performance of the SS and QR method for pictures impaired by Gaussian blur. The research goal is, on one hand, to analyze the advantages and disadvantages of both methods for quality assessment and, on the other, to make quality data of blur impaired images publicly available. The obtained results show that the confidence intervals of the QR scores are narrower than those of the SS scores. This indicates that the QR method enhances consistency across assessors. Moreover, QR scores exhibit a higher linear correlation with the distortion applied. In summary, for the purpose of building datasets of subjective quality, the QR approach seems promising from the viewpoint of both consistency and repeatability.

Redi, Judith; Liu, Hantao; Alers, Hani; Zunino, Rodolfo; Heynderickx, Ingrid

2010-01-01

146

Exploration of preterm birth rates using the public health exposome database and computational analysis methods.  

PubMed

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother's age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births. PMID:25464130

Kershenbaum, Anne D; Langston, Michael A; Levine, Robert S; Saxton, Arnold M; Oyana, Tonny J; Kilbourne, Barbara J; Rogers, Gary L; Gittner, Lisaann S; Baktash, Suzanne H; Matthews-Juarez, Patricia; Juarez, Paul D

2014-12-01

147

Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods  

PubMed Central

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births. PMID:25464130

Kershenbaum, Anne D.; Langston, Michael A.; Levine, Robert S.; Saxton, Arnold M.; Oyana, Tonny J.; Kilbourne, Barbara J.; Rogers, Gary L.; Gittner, Lisaann S.; Baktash, Suzanne H.; Matthews-Juarez, Patricia; Juarez, Paul D.

2014-01-01

148

Database for chicken full-length cDNAs.  

PubMed

The generation of full-length cDNA databases is essential for functional genomics studies as well as for correct annotation of species genomic sequences. Human and mouse full-length cDNA projects have provided the biomedical research community with a large amount of gene information. Recent completion of the chicken genome sequence draft now enables a similar full-length cDNA project to be initiated for this species. In this report, we introduce the development of a chicken full-length cDNA database, which will facilitate future research work in this biological system. In this project, chicken expressed sequence tags (ESTs) were aligned onto human and mouse full-length cDNAs (or open reading frames) on the basis of their similarity. More than 588,000 chicken ESTs were aligned to approximately 170,000 full-length human and mouse templates obtained from the NEDO, RIKEN, and MGC databases. Many of these templates have known biological functions, and their orthologous chicken genes in the EMBL database are also provided in our database, which is available at http://bioinfo.hku.hk/chicken/. We will continue to collect known chicken full-length cDNAs to update the database for public use. The cDNA alignment results presented herein and on our database will be useful for animal science and veterinary researchers wishing to clone and to confirm full-length chicken cDNAs of interest. PMID:17105754

Wang, Yong; Wang, Zhenggang; Li, Juan; Wang, Yajun; Leung, Frederick C C

2007-01-17

149

Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies.  

PubMed

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H C; De Keersmaecker, Sigrid C J

2014-12-01

150

Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies  

PubMed Central

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at ?20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

2014-01-01

151

Estimation of water table based on geomorphologic and geologic conditions using public database of geotechnical information over Japan  

NASA Astrophysics Data System (ADS)

Water table provides important information for the evaluation of groundwater resource. Recently, the estimation of water table in wide area is required for effective evaluation of groundwater resources. However, evaluation process is met with difficulties due to technical and economic constraints. Regression analysis for the prediction of groundwater levels based on geomorphologic and geologic conditions is considered as a reliable tool for the estimation of water table of wide area. Data of groundwater levels were extracted from the public database of geotechnical information. It was observed that changes in groundwater level depend on climate conditions. It was also observed and confirmed that there exist variations of groundwater levels according to geomorphologic and geologic conditions. The objective variable of the regression analysis was groundwater level. And the explanatory variables were elevation and the dummy variable consisting of group number. The constructed regression formula was significant according to the determination coefficients and analysis of the variance. Therefore, combining the regression formula and mesh map, the statistical method to estimate the water table based on geomorphologic and geologic condition for the whole country could be established.

Koshigai, Masaru; Marui, Atsunao

152

Drinking Water Treatability Database (Database)  

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

153

DNA barcoding for plants.  

PubMed

DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing. PMID:25373752

de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte

2015-01-01

154

GEOBASE: Israel Regional Database  

NSDL National Science Digital Library

GEOBASE is a searchable database that contains data extracted from Israel's Central Bureau of Statistics, statistical publications, public service records, local databases, and summaries from individual level datasets. GEOBASE provides regularly updated annual and quarterly series on numerous topics, including economic activities, labor and wages, population, transportation, tourism, housing, and education.

155

BioModels Database  

NSDL National Science Digital Library

Hosted by the European Bioinformatics Institute, the BioModels Database is a collaborative, "new effort to develop a data resource that will allow biologist to store, search and retrieve published mathematical models of biological interests. The models in the BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc." The website allows visitors to browse and search the Database for models. The site also provides information about submitting models for the Database. It should be noted that submitted models must undergo tests conducted by BioModels Database curators before they are incorporated. [NL

156

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 (Received for publication, June 12, 1998, and in revised form, November 16, 1998)  

E-print Network

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 Protein* (Received for publication Rad51 protein is the para- digm for eukaryotic ATP-dependent DNA strand ex- change proteins. To explain some of the unique charac- teristics of DNA strand exchange promoted by Rad51 protein, when

Kowalczykowski, Stephen C.

157

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4, 2003, and in revised form, October 3, 2003  

E-print Network

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4A proteins of Escherichia coli (Ec) and Deino- coccus radiodurans (Dr) both promote a DNA strand exchange- stranded DNA-binding protein (SSB). In the absence of SSB, the initiation of strand exchange is greatly en

Cox, Michael M.

158

Aviation Safety Issues Database  

NASA Technical Reports Server (NTRS)

The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

Morello, Samuel A.; Ricks, Wendell R.

2009-01-01

159

Multiparameter Intelligent Monitoring in Intensive Care Ii (Mimic-Ii): A Public-Access Intensive Care Unit Database  

E-print Network

Objective: We sought to develop an intensive care unit research database applying automated techniques to aggregate high-resolution diagnostic and therapeutic data from a large, diverse population of adult intensive care ...

Saeed, Mohammed

160

Human Mitochondrial Protein Database  

NSDL National Science Digital Library

The Human Mitochondrial Protein Database (HMPDb) conveniently consolidates information from a number of other databases, including GenBank, Online Mendelian Inheritance in Man, and the Human Mitochondrial Genome Database. HMPDb "is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases" as well. Features include a general database search, a graphical tool for visualizing the mitochondrial DNA sequences, and 3D structures for mitochondrial proteins. Users are welcome to contact the National Institute of Standards and Technology with corrections or other information relating to the database.

161

Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography  

Microsoft Academic Search

Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west\\u000a Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in\\u000a HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1

H. Pfeiffer; B. Brinkmann; J. Hühne; B. Rolf; A. A. Morris; R. Steighner; M. M. Holland; P. Forster

1999-01-01

162

A New Model for Providing Cell-Free DNA and Risk Assessment for Chromosome Abnormalities in a Public Hospital Setting  

PubMed Central

Objective. Cell-free DNA (cfDNA) offers highly accurate noninvasive screening for Down syndrome. Incorporating it into routine care is complicated. We present our experience implementing a novel program for cfDNA screening, emphasizing patient education, genetic counseling, and resource management. Study Design. Beginning in January 2013, we initiated a new patient care model in which high-risk patients for aneuploidy received genetic counseling at 12 weeks of gestation. Patients were presented with four pathways for aneuploidy risk assessment and diagnosis: (1) cfDNA; (2) integrated screening; (3) direct-to-invasive testing (chorionic villus sampling or amniocentesis); or (4) no first trimester diagnostic testing/screening. Patients underwent follow-up genetic counseling and detailed ultrasound at 18–20 weeks to review first trimester testing and finalize decision for amniocentesis. Results. Counseling and second trimester detailed ultrasound were provided to 163 women. Most selected cfDNA screening (69%) over integrated screening (0.6%), direct-to-invasive testing (14.1%), or no screening (16.6%). Amniocentesis rates decreased following implementation of cfDNA screening (19.0% versus 13.0%, P < 0.05). Conclusion. When counseled about screening options, women often chose cfDNA over integrated screening. This program is a model for patient-directed, efficient delivery of a newly available high-level technology in a public health setting. Genetic counseling is an integral part of patient education and determination of plan of care. PMID:25101177

Wallerstein, Robert; Jelks, Andrea; Garabedian, Matthew J.

2014-01-01

163

Development of a DNA microarray to detect antimicrobial resistance genes identified in the national center for biotechnology information database  

Technology Transfer Automated Retrieval System (TEKTRAN)

High density genotyping techniques are needed for investigating antimicrobial resistance especially in the case of multi-drug resistant (MDR) isolates. To achieve this all antimicrobial resistance genes in the NCBI Genbank database were identified by key word searches of sequence annotations and the...

164

Who owns what? Private ownership and the public interest in recombinant DNA technology in the 1970s.  

PubMed

This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising from public support would provide a powerful means to liberate biomedical discoveries for public benefit. This articulation of the causal link between private ownership and the public interest, it is argued, justified a new set of expectations about the use of research results arising from government or public support, in which commercialization became a new public obligation for academic researchers. By highlighting the broader economic and legal shifts that prompted the reconfiguration of the ownership of public knowledge in late twentieth-century American capitalism, the essay examines the threads of policy-informed legal ideas that came together to affirm private ownership of biomedical knowledge as germane to the public interest in the coming of age of biotechnology and genetic medicine. PMID:22073770

Yi, Doogab

2011-09-01

165

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.  

PubMed

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2013-01-01

166

Morchella MLST database  

Technology Transfer Automated Retrieval System (TEKTRAN)

Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current datab...

167

Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data  

PubMed Central

The database of Gene Co-Regulation (dGCR) is a web tool for the analysis of gene relationships based on correlated patterns of gene expression over publicly available transcriptional data. The motivation behind dGCR is that genes whose expression patterns correlate across many experiments tend to be co-regulated and hence share biological function. In addition to revealing functional connections between individual gene pairs, extended sets of co-regulated genes can also be assessed for enrichment of gene ontology classes and interaction pathways. This functionality provides an insight into the biological function of the query gene itself. The dGCR web tool extends the range of expression data curated by existing co-regulation databases and provides additional insights into gene function through the analysis of pathways, gene ontology classes and co-regulation modules. PMID:25628763

Williams, Gareth

2015-01-01

168

The Zoonoses Database-A HyperCard™ Stack on the Macintosh™ Computer for Teaching Veterinary Epidemiology and Public Health  

PubMed Central

For the past 2 years second-year veterinary students have used a HyperCard-based Zoonoses Database to abstract, store and retrieve information on zoonotic diseases. Each student was required to review the veterinary literature for information about one zoonotic disease and enter the information into a HyperCard template which summarized epidemiologic aspects of the disease. A total of 99 diseases are included in the Zoonoses Database. To use this resource in problem-solving, students formed mock 2 to 6 person veterinary practices. Student “practice groups” were then assigned one of 24 case histories and asked to form a rule-out list, select the most probable disease, and provide advice to the client regarding the zoonotic potential of the disease in question. We will continue to expand the database and link life cycles to it.

Hungerford, Laura L.; Smith, Ronald P.; Smith, Ronald D.

1990-01-01

169

DNA  

NSDL National Science Digital Library

In this activity, students extract DNA from their cheek cells and relate the steps in the procedure to the characteristics of cells and biological molecules. Students learn key concepts about the function of DNA during the intervals required for the extraction procedure. A second optional section develops student understanding of the fundamentals of DNA structure, function and replication; this section includes hands-on modeling of DNA replication. This activity, together with our activity, "From Gene to Protein - Transcription and Translation", can be used to teach the basic concepts of molecular biology.

Jennifer Doherty

170

DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents and Investigations  

E-print Network

and individual identities of a mountain lion (Puma concolor) and a bobcat (Lynx rufus) from swab samples Avenue, Davis, CA 95616. Ernest phone (530) 754-8245 and email hbernest@ucdavis.edu. Key Words: Puma concolor, bobcat, forensic, genetics, DNA techniques, noninvasive sampling, fecal DNA, prey swab DNA

Ernest, Holly

171

DNA.  

ERIC Educational Resources Information Center

Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

Felsenfeld, Gary

1985-01-01

172

76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...  

Federal Register 2010, 2011, 2012, 2013, 2014

...public notice by publishing a drug's generic or trade name upon orphan designation. Where a designated drug does not have a generic or trade name, publishing...orphan-drug designation. If a drug has no generic or trade name,...

2011-08-30

173

Ionic Liquids Database- (ILThermo)  

National Institute of Standards and Technology Data Gateway

SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

174

Shakespeare Database Project  

NSDL National Science Digital Library

The Shakespeare database project at Westf=8Alische Wilhelms-Universitat Munster, Germany posts project news and information on publications its own WWW Home-Page. There is also a preview on the Shakespeare Database CD-ROM to be presented at the 1994 Frankfurt Bookfair.

175

ii The query may not be an exact match or even partial match with any data in the database, but since DNA annealing a nity methods work  

E-print Network

, etc. 1 Introduction 1.1 Recombinant DNA Technology DNA as a Storage Media. Recall that DNA is a linear at concentrations of about 5 grams of DNA per liter of water. Recombinant DNA Technology. Biotechnological methods, which are collectively known as recombinant DNA technology, have been developed for a wide class of op

Reif, John H.

176

DNA  

ERIC Educational Resources Information Center

This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

Stent, Gunther S.

1970-01-01

177

The public Human Genome Project: mapping the genome, sequencing, and reassembly, 3D animationSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

DNAi location: Genome>The Project>putting it together>Animations>Hierarchical shotgun (public) Mapping the genome AND Sequencing and assembly This animation shows how the human genome was sequenced using the 'hierarchical shotgun' method of the public Human Genome Project. All the base pairs in our DNA are represented as letters on pieces of paper.

2008-10-06

178

Current research status, databases and application of single nucleotide polymorphism.  

PubMed

Single Nucleotide Polymorphisms (SNPs) are the most frequent form of DNA variation in the genome. SNPs are genetic markers which are bi-allelic in nature and grow at a very fast rate. Current genomic databases contain information on several million SNPs. More than 6 million SNPs have been identified and the information is publicly available through the efforts of the SNP Consortium and others data bases. The NCBI plays a major role in facillating the identification and cataloging of SNPs through creation and maintenance of the public SNP database (dbSNP) by the biomedical community worldwide and stimulate many areas of biological research including the identification of the genetic components of disease. In this review article, we are compiling the existing SNP databases, research status and their application. PMID:21717869

Javed, R; Mukesh

2010-07-01

179

Rainfall Simulation Database  

NSDL National Science Digital Library

The British Geomorphological Research Group maintains this rainfall simulation database site. The database includes information about rainfall simulators, as well as their set-up and use. Currently, the database is divided into laboratory, field, and dual-purpose (lab and field) rainfall simulators. For each simulator in the database, users will find information on: "Simulator identification; Contact information; Specification of simulator; performance of simulator; Table of intensities and rainfall characteristics; Costs; Summary of research conducted using the simulator; Publications; and Additional comments." A section on simulation calibration is planned, and a form is provided for those wishing to contribute simulators to the database. A lengthy selection of related references adds to the utility of the database.

180

Using data from the public project, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Using data from the public project Craig Venter, leader of the private effort at Celera Genomics, speaks about his company's reliance on the public data for reassembly of the Celera sequence.

2008-10-06

181

Nanotechnology Database  

NSDL National Science Digital Library

Sponsored by the National Science Foundation and housed at the Loyola College in Maryland's International Technology Research Institute the Nanotechnology Database is a source of online information on major research centers, funding agencies, major reports, and books dealing with nanotechnology. The resources listed here are carefully selected and reviewed. The site is expected to grow with the continued support and updates from organizations and individuals in the field of nanotechnology. The list of resources is divided into the following categories: Academic, Industry, Government Laboratories, Government Agencies, Professional Societies, Non-Profit Organizations, Books, Periodicals, Reports, and Conferences. Each listing provides a brief summary (taken from that Website) and hyperlink to the resource (note: the book list links mostly take users to online booksellers). A submission form allows users to add a relevant organization or publication.

182

Taking Nutrigenomics to the Public: Genome Health Clinics for Personalised DNA Damage Prevention  

Microsoft Academic Search

It is becoming increasingly evident that (a) risk for developmental and degenerative disease increases with more DNA damage, which in turn is dependent on nutritional status, and (b) the optimal concentration of micronutrients for prevention of genome damage is also dependent on genetic polymorphisms that alter the function of genes involved directly or indirectly in the uptake and metabolism of

Michael Fenech

183

Public concern over genetic manipulation, Alexander CapronSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Alexander Capron DNAi Location:Manipulation>Revolution>players>The controversy The Frankenstein factor Alexander Capron, a lawyer and specialist in bioethics, talks about how fear of Frankenstein captured the public fancy.

2008-10-06

184

The public Human Genome Project, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>The project>players>money Threatening their funding Craig Venter speaks about the public sector's reaction to his plans to sequence the genome at a private company, Celera Genomics.

2008-10-06

185

Buffmap Database  

NSDL National Science Digital Library

The Institut National de Recherche Agronomique (France) provides online databases of genomes for several organisms, including Buffalo. The database is updated as more data become available, and provide records on loci, genes, microsatellites, polymorphisms, probes, enzymes, homologue loci, alleles, primers, references, and links to external databases. Instructions for submitting data to the databases are provided on-site.

186

Publications  

NSDL National Science Digital Library

The Nitrogen and Phosphorus Knowledge Web page is offered by Iowa State University Extension and the College of Agriculture. The publications page contains links to various newsletters, articles, publications, power point presentations, links to governmental publications, and more. For example, visitors will find articles written on phosphorous within the Integrated Crop Management Newsletter, power point presentations on Nitrogen Management and Carbon Sequestration, and links to other Iowa State University publications on various subjects such as nutrient management. Other links on the home page of the site contain soil temperature data, research highlights, and other similarly relevant information for those in similar fields.

1969-12-31

187

YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae.  

PubMed

Saccharomyces cerevisiae, i.e. baker's yeast, is a widely studied model organism in eukaryote genetics because of its simple protocols for genetic manipulation and phenotype profiling. The high abundance of publicly available data that has been generated through diverse 'omics' approaches has led to the use of yeast for many systems biology studies, including large-scale gene network modeling to better understand the molecular basis of the cellular phenotype. We have previously developed a genome-scale gene network for yeast, YeastNet v2, which has been used for various genetics and systems biology studies. Here, we present an updated version, YeastNet v3 (available at http://www.inetbio.org/yeastnet/), that significantly improves the prediction of gene-phenotype associations. The extended genome in YeastNet v3 covers up to 5818 genes (?99% of the coding genome) wired by 362 512 functional links. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (?2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links. PMID:24165882

Kim, Hanhae; Shin, Junha; Kim, Eiru; Kim, Hyojin; Hwang, Sohyun; Shim, Jung Eun; Lee, Insuk

2014-01-01

188

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  

SciTech Connect

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

2005-08-13

189

DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES  

EPA Science Inventory

The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

190

DNA . DNA  

E-print Network

-base non 1-Base non Watson-Crick DNA Hybridization Simulation O O DNA Hybridization SimulationIntelligence Lab. School of Computer Science and Engineering, Seoul National University 1-Base non Watson-Crick DNA DNA . #12;Watson-Crick base pair 1-base dangling end hybridization . PCR

191

The CIPIC HRTF database  

Microsoft Academic Search

This paper describes a public-domain database of high-spatial-resolution head-related transfer functions measured at the UC Davis CIPIC Interface Laboratory and the methods used to collect the data.. Release 1.0 (see http:\\/\\/interface.cipic.ucdavis.edu) includes head-related impulse responses for 45 subjects at 25 different azimuths and 50 different elevations (1250 directions) at approximately 5° angular increments. In addition, the database contains anthropometric measurements

V. R. Algazi; R. O. Duda; D. M. Thompson; C. Avendano

2001-01-01

192

The EMBL nucleotide sequence database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is

Guenter Stoesser; Wendy Baker; Alexandra Van Den Broek; Evelyn Camon; Maria Garcia-pastor; Carola Kanz; Tamara Kulikova; Vincent Lombard; Rodrigo Lopez; Helen E. Parkinson; Nicole Redaschi; Peter Sterk; Peter Stoehr; Mary Ann Tuli

2001-01-01

193

Hydrocarbon Impacts Database  

NSDL National Science Digital Library

The Hydrocarbon Impacts (HI) database is a subset of the University of Calgary's Arctic Institute of North America's Arctic Science and Technology Information System database. More than 5,100 records describe "publications and research projects about the environmental impacts, socio-economic effects and regulation of hydrocarbon exploration, development and transportation in northern Canada." Users can search by record type, keyword, subject code, geographic code, author, and year, as well as an advanced search feature to locate the information. Well designed and easy to use, the database provides those interested in this narrow subject field a helpful resource.

194

Database of Zeolite Structures  

NSDL National Science Digital Library

The Database of Zeolite Structures is provided by the Structure Commission of the International Zeolite Association. Links include an Atlas of Zeolite Framework Types, Collection of Simulated XRD Powder Patterns for Zeolites, Catalog of Disordered Zeolite Structures, Schemes for Building Zeolite Framework Models, and Zeolite Structure References, as well as various publications. The database can be searched or browsed, and contains several useful tools such as the "input your data" link, which allows the user to enter crystallographic data not available in the database and generate the diffraction pattern.

195

Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy  

SciTech Connect

A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a reference value. To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

Strait, R.S.; Pearson, P.K.; Sengupta, S.K.

2000-03-14

196

Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy  

DOEpatents

A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a "reference value." To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

Strait, Robert S. (Oakland, CA); Pearson, Peter K. (Livermore, CA); Sengupta, Sailes K. (Livermore, CA)

2000-01-01

197

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software  

PubMed Central

Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely. PMID:23088273

Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

2014-01-01

198

Russian Regional Database  

NSDL National Science Digital Library

The Centre for the Study of Public Policy (CSPP) at the University of Strathclyde, Glasgow has created a new online database that presents a comparative overview of eleven Russian regions: Central, Central Black Earth, East Siberia, Far East, North Caucasus, Northern, North-west, Urals, Volga, Volgo-Vyatka, and West Siberia. The database provides data garnered from official government statistics and public opinion surveys to compare indicators that measure economic competitiveness; labor market change; and social cohesion, exclusion, and stability. The data are accompanied by analysis written by Professor Richard Rose.

1998-01-01

199

Biofuel Database  

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

200

FACILITY DATABASE  

Cancer.gov

January 2008 LASP FACILTY Database Form 5.000 Issue Reporting Form This form is used to report data and/or program related issues regarding the FACILITY database, Supplemental, or the LASP Online Access System. Before submitting this form,

201

FACILITY DATABASE  

Cancer.gov

LASP Administrative Use Only Data Entry Start Date _______________ July 2007 LASP FACILTY Database Form 1.000 FACILITY DATABASE Principal Investigator – Data Entry Requirements This form is used to identify the level of data that each investigator

202

JAMSTEC Databases  

NSDL National Science Digital Library

From the Japan Marine Science and Technology Center (JAMSTEC) comes the JAMSTEC databases site. Visitors can access several databases and data sites including the Deep Seafloor Image Database, Japan ARGO Delayed-mode Database, the J-CAD Compact Arctic Drifter, MIRAI Data Web, Research Results Report System, Submarine Cable Data Center, and the TRITON Buoy Data Web site. All provide marine science related information from Japan and around the world.

2002-01-01

203

Database Administrator  

ERIC Educational Resources Information Center

The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

Moore, Pam

2010-01-01

204

Annual Review of Database Development: 1992.  

ERIC Educational Resources Information Center

Reviews recent trends in databases and online systems. Topics discussed include new access points for established databases; acquisitions, consolidations, and competition between vendors; European coverage; international services; online reference materials, including telephone directories; political and legal materials and public records;…

Basch, Reva

1992-01-01

205

USDA NATIONAL NUTRIENT DATABASE FOR STANDARD REFERENCE  

EPA Science Inventory

The USDA Nutrient Database for Standard Reference (SR) is the major source of food composition data in the United States. It provides the foundation for most food composition databases in the public and private sectors....

206

Public Databases Supporting Computational Toxicology  

EPA Science Inventory

A major goal of the emerging field of computational toxicology is the development of screening-level models that predict potential toxicity of chemicals from a combination of mechanistic in vitro assay data and chemical structure descriptors. In order to build these models, resea...

207

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database-the quality controlled standard tool for routine identification of human and animal pathogenic fungi.  

PubMed

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens. PMID:25802363

Irinyi, Laszlo; Serena, Carolina; Garcia-Hermoso, Dea; Arabatzis, Michael; Desnos-Ollivier, Marie; Vu, Duong; Cardinali, Gianluigi; Arthur, Ian; Normand, Anne-Cécile; Giraldo, Alejandra; da Cunha, Keith Cassia; Sandoval-Denis, Marcelo; Hendrickx, Marijke; Nishikaku, Angela Satie; de Azevedo Melo, Analy Salles; Merseguel, Karina Bellinghausen; Khan, Aziza; Parente Rocha, Juliana Alves; Sampaio, Paula; da Silva Briones, Marcelo Ribeiro; E Ferreira, Renata Carmona; de Medeiros Muniz, Mauro; Castańón-Olivares, Laura Rosio; Estrada-Barcenas, Daniel; Cassagne, Carole; Mary, Charles; Duan, Shu Yao; Kong, Fanrong; Sun, Annie Ying; Zeng, Xianyu; Zhao, Zuotao; Gantois, Nausicaa; Botterel, Françoise; Robbertse, Barbara; Schoch, Conrad; Gams, Walter; Ellis, David; Halliday, Catriona; Chen, Sharon; Sorrell, Tania C; Piarroux, Renaud; Colombo, Arnaldo L; Pais, Célia; de Hoog, Sybren; Zancopé-Oliveira, Rosely Maria; Taylor, Maria Lucia; Toriello, Conchita; de Almeida Soares, Célia Maria; Delhaes, Laurence; Stubbe, Dirk; Dromer, Françoise; Ranque, Stéphane; Guarro, Josep; Cano-Lira, Jose F; Robert, Vincent; Velegraki, Aristea; Meyer, Wieland

2015-05-01

208

National Ambient Radiation Database  

SciTech Connect

The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

Dziuban, J.; Sears, R.

2003-02-25

209

Neogene Mammal Database  

NSDL National Science Digital Library

There are plenty of mammal databases that deal with existing taxonomies and such, but where can one go to find information about land mammal taxa from the Eurasian Miocene to Pleistocene periods? They need look no further than this fine website, which provides access to such material, courtesy of an international advisory board, headed by Mikael Fortelius of the University of Helsinki. First-time visitors may want to look over the data conventions section first. Here they can learn about the proper use of taxonomic fields, and also view such taxonomic examples from the database. Users may also want to look over the browsing section, as it serves as a good orientation to effectively using the database. For those engaged in scholarly endeavors related to the field, there is also a publications section that offers access to recent works that draw on this rather voluminous database.

210

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/), maintained at the European Bioinformatics Institute (EBI), incorporates, organ- izes and distributes nucleotide sequences from public sources. The database is a part of an inter- national collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is

Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra Van Den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle Mchale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2004-01-01

211

IOPI Database of Plant Databases  

NSDL National Science Digital Library

The International Organization for Plant Information (IOPI), a Commission of the International Union of Biological Sciences (IUBS), manages the Database of Plant Databases (DPD). The DPD is a global list of plant databases including Taxonomic databases ("with systematic information on families or genera, or for Flora projects"); Collection catalogs (usually of herbaria); and DELTA datasets (DELTA is "the Description Language for Taxonomy, a data format for character data, used for identification, key construction and the generation of descriptions."). The DPD may be searched using numerous specified fields, or it may be viewed in its entirety -- by Database Name, Host Name, or Host Country. Though bare bones in appearance, this extensive database contains a gold mine of information, with hundreds of hyperlinks to valuable plant databases.

212

The EUVE satellite survey database  

NASA Technical Reports Server (NTRS)

The EUVE survey database contains fundamental science data for 9000 potential source locations (pigeonholes) in the sky. The first release of the Bright Source List is now available to the public through an interface with the NASA Astrophysical Data System. We describe the database schema design and the EUVE source categorization algorithm that compares sources to the ROSAT Wide Field Camera source list.

Craig, N.; Chen, T.; Hawkins, I.; Fruscione, A.

1993-01-01

213

Beyond the cold hit: measuring the impact of the national DNA data bank on public safety at the city and county level.  

PubMed

Over the past decade, the Combined DNA Index System (CODIS) has increased solvability of violent crimes by linking evidence DNA profiles to known offenders. At present, an in-depth analysis of the United States National DNA Data Bank effort has not assessed the success of this national public safety endeavor. Critics of this effort often focus on laboratory and police investigators unable to provide timely investigative support as a root cause(s) of CODIS' failure to increase public safety. By studying a group of nearly 200 DNA cold hits obtained in SFPD criminal investigations from 2001-2006, three key performance metrics (Significance of Cold Hits, Case Progression & Judicial Resolution, and Potential Reduction of Future Criminal Activity) provide a proper context in which to define the impact of CODIS at the City and County level. Further, the analysis of a recidivist group of cold hit offenders and their past interaction with law enforcement established five noteworthy criminal case resolution trends; these trends signify challenges to CODIS in achieving meaningful case resolutions. CODIS' effectiveness and critical activities to support case resolutions are the responsibility of all criminal justice partners in order to achieve long-lasting public safety within the United States. PMID:20579236

Gabriel, Matthew; Boland, Cherisse; Holt, Cydne

2010-01-01

214

Introduction to Database Database Systems Lecture 1  

E-print Network

of information · Database systems give a set of tools for storing, searching and managing this information with the database system · Database Administrator (DBA) · Designs & manages the database system · Database systems programmer · Writes the database software itself #12;Database Management Systems · A database is a collection

Alechina, Natasha

215

Addition of a breeding database in the Genome Database for Rosaceae.  

PubMed

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox. PMID:24247530

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

216

Image Databases.  

ERIC Educational Resources Information Center

Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

Pettersson, Rune

217

Maize databases  

Technology Transfer Automated Retrieval System (TEKTRAN)

This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

218

NIOSHTIC DATABASE  

EPA Science Inventory

NIOSHTIC Database is a bibliographic database of literature in the field of occupational safety and health. English language technical journals provide approximately 35 percent of the additions to NIOSHTIC? annually. Retrospective information, some of which is from the 19th centu...

219

NSFC Databases  

NSDL National Science Digital Library

The National Environmental Services Center (NESC) is based at West Virginia University and "serves as a clearinghouse for information about drinking water, wastewater, environmental training, and solid waste management in communities serving fewer than 10,000 individuals." As part of the NSFC larger Web site, the Databases page offers three online databases that can be accessed free after an initial registration. The Regulations Database contains copies of regulations for onsite wastewater treatment systems in 48 states, the Bibliographic Database stores thousands of articles dealing with onsite and small community wastewater issues, and the Manufacturers and Consultants Database houses a list of industry contacts for wastewater products and consulting services. Much more is available within the larger NSFC site and readers are encouraged to take a look through its contents.

220

Cancer Control Publications 1998-2011: FAQ  

Cancer.gov

CC Publications is a searchable database developed by DCCPS that includes staff, contract investigators, and grantee publications. This database demonstrates the depth and breadth of research publications in cancer control and population sciences funded by NCI.

221

Assessing the Potential Public Health Impacts of Next Generation Foods Derived from Recombinant DNA Technology: A Case Study of Omega3 Fatty Acids Enhanced Vegetable Oils  

Microsoft Academic Search

We assessed the potential public health impacts of foods derived from recombinant DNA technology that have been modified to have improved nutrient profiles using omega-3-enhanced vegetable oils as an example. Other examples of crops in development include canola plants with increased vitamin C and rice with higher levels of beta-carotene. The change in consumption of omega-3 fatty acids if vegetable

Richard A. Forshee; Maureen L. Storey; Patricia A. Anderson

2009-01-01

222

DNA Barcoding  

NSDL National Science Digital Library

This is a two-part animation. Â?DNA Barcoding, Part 1,Â? provides an overview of how DNA barcoding of animals can be used to identify an unknown sample or discover a new species. Cytochrome c oxidase subunit 1 (COI) is found in the mitochondria as part of the electron transport chain. The COI gene is used for DNA barcoding. Just like a barcode on an item in a grocery store identifies a product, a DNA barcode (determined by DNA sequencing) is used to identify species. Part 1 run time: 1 minute, 40 seconds. Â?DNA Barcoding, Part 2Â? details how small tissue samples are used for DNA barcoding, including a review of the laboratory and bioinformatics steps used in barcoding: DNA purification, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing and analysis, and DNA sequence identification using the Basic Local Alignment Search Tool (BLAST) or the Barcode of Life Database (BOLD). Part 2 run time: 4 minutes, 15 seconds. Animation is closed captioned.

2012-10-22

223

Alcohol Industry & Policy Database  

NSDL National Science Digital Library

The Marin Institute for the Prevention of Alcohol and Other Drug Problems maintains the Alcohol Industry & Policy Database, which contains bibliographic citations and abstracts for more than 13,000 articles and news stories on the alcohol beverage industry, alcohol policy, and the prevention of alcohol-related problems. The citations in the database span from 1991 to the present and are updated monthly. Users may conduct cross-field queries of the database by keywords, subject headings, company name, and publication date. The search facility includes Word Wheels, which are interactive Java applets that help users to identify indexed terms quickly, thereby "eliminat[ing] trial-and-error searching [and] produc[ing] more accurate searches."

Marin Institute for the Prevention of Alcohol and Other Drug Problems.

224

Hospital Records Database  

NSDL National Science Digital Library

This new joint project from the Wellcome Trust and the UK Public Record Office helps researchers locate records of hospitals all over the UK. The database currently contains over 2,800 entries and may be searched by hospital or town name. Information contained in the database includes administrative details of the hospitals, location and covering dates of administrative and clinical records, and the existence of lists, catalogs or other finding aids. A sample search for "royal" under hospital name returned 210 records, and one for "Manchester" under town name produced 124 returns. While the target audience of this database -- researchers in British medical history -- is rather specialized, this new resource will prove extremely useful for these scholars and their students.

225

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

Calm, J.M.

1992-04-30

226

BIOMARKERS DATABASE  

EPA Science Inventory

This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

227

ASC Publications  

NSDL National Science Digital Library

The University of Wisconsin's Applied Superconductivity Center (ASC) has a publications page with a good selection of online papers on superconductivity. The page contains a searchable publications database, a list of all ASC papers online, and a list of papers supported by the National Science Foundation.

228

Tsunami Database  

NSDL National Science Digital Library

The Tsunami Database is a global digital database containing information on more than 2000 tsunamis maintained by the National Geophysical Data Center. This is an interactive site; the user is asked to enter search parameters such as date, latitude and longitude, cause of the tsunami - earthquake, landslide, volcano, or all combined - magnitude, and death. Information is then generated on tsunamis that match that data. The National Geophysical Data Center also maintains an historic slide set collection of tsunami damage.

229

A Transaction Mechanism for Engineering Design Databases  

Microsoft Academic Search

One primary difference between transactions in an engineering design environment and those in conventional business applications is that an engineering transaction typically lasts a much longer time. Existing proposals for supporting the long-lived engineering transactions are all based on the public\\/private database architec- ture, in which a transaction checks out design objects from the public database, modifies them, and checks

Won Kim; Raymond A. Lorie; Dan Mcnabb; Wil Plouffe

1984-01-01

230

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:8594557

Cariello, N F; Douglas, G R; Soussi, T

1996-01-01

231

National Tourism Database  

NSDL National Science Digital Library

Developed by the Michigan State University Extension Tourism Area of Expertise and the National Tourism Education Design Team, this site contains information on numerous resources related to tourism education, including bulletins, research reports, videos, and training programs. Nearly 100 of the documents featured are full-text. Users can browse the database by topic or browse or search by keyword. A separate list of the full-text publications is also provided. A useful site for students and professionals in the tourism industry.

232

DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database  

Microsoft Academic Search

Caves represent a unique environment in which to study subsurface geomicrobial interactions and processes. One of the primary techniques used to study such geologic samples is molecular phylogenetic analysis, but this technique is hampered by low microbial biomass and calcium in the host rock, often leading to poor and irreproducible DNA extraction. We describe an improved protocol to recover extremely

H. A. Barton; N. M. Taylor; B. R. Lubbers; A. C. Pemberton

2006-01-01

233

Comparing the public and private sequencing projects, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Comparing public and private Craig Venter, the leader of the private genome effort at Celera Genomics, talks about the differences between the public and private approaches.

2008-10-06

234

MetaBase--the wiki-database of biological databases.  

PubMed

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

Bolser, Dan M; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Del Angel, Victoria Dominguez; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J; Clements, Dave; Renfro, Daniel P; Bhak, Daeui; Bhak, Jong

2012-01-01

235

INVADERS Database  

NSDL National Science Digital Library

Based at the University of Montana and directed by Dr. Peter Rice, the INVADERS Database is "a comprehensive database of exotic plant names and weed distribution records for five states in the northwestern United States." Designed for use by land management and weed regulatory agencies, INVADERS uses a query interface (plant name or location) to sort and display information. Data are updated regularly so as to increase the chance of detecting and halting the rapid spread of alien weeds. Highlights of the site include the noxious weed listings for all US states and six Canadian provinces, historic distribution records against which to compare current plant distributions, and summary statistics such as the number of invasive species detected per state or a summary of the 120 year invasion, among others. The INVADERS database will prove both interesting and useful to managers and academics, alike.

236

Solubility Database  

National Institute of Standards and Technology Data Gateway

SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

237

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database  

SciTech Connect

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

2010-01-27

238

Avibase: The World Bird Database  

NSDL National Science Digital Library

This database provides information on all birds of the world, featuring information on thousands of species and subspecies of birds such as taxonomy, names and synonyms in various languages, photos, distribution maps, and links to additional information from other websites. The database is searchable by keyword or term, exact name, language, year of publication, and other parameters. There is also a search by taxonomic family, a set of checklists by geographic region, and a blog for ornithological discussions.

Denis Lepage

239

NASA STI Database, Aerospace Database and ARIN coverage of 'space law'  

NASA Technical Reports Server (NTRS)

The space-law coverage provided by the NASA STI Database, the Aerospace Database, and ARIN is briefly described. Particular attention is given to the space law content of the two Databases and of ARIN, the NASA Thesauras space law terminology, space law publication forms, and the availability of the space law literature.

Buchan, Ronald L.

1992-01-01

240

Calibrating Databases.  

ERIC Educational Resources Information Center

Reports on study that used set of measures for characterizing performance with different databases and set of hypotheses for predicting search difficulties based on cognitive processes involved in decision-making aspects of information search. Highlights include confidence assessment, system design criteria, transparency, metatransparency, and…

Fischhoff, Baruch; MacGregor, Donald

1986-01-01

241

Mineralogy Database  

NSDL National Science Digital Library

This is a large database of minerals that can be sorted either alphabetically or arranged systematically. Users can access minerals by name, elements, sulfides, halides, oxides, carbonates, sulfates, phosphates, silicates, organic minerals, or by variety. Once located, the properties of the mineral are displayed, including its chemical formula, crystal system, and location. Users can also access photos of minerals.

242

FACILITY DATABASE  

Cancer.gov

LASP Administrative Use Only Data Entry Start Date _______________Investigator Data RequirementsJuly 2007 LASP FACILTY Database Form 1.000This form is used to identify the level of data that each investigator [and his/her staff] will require for entry

243

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:9399835

Cariello, N F; Douglas, G R; Gorelick, N J; Hart, D W; Wilson, J D; Soussi, T

1998-01-01

244

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.  

PubMed

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database. PMID:9016522

Cariello, N F; Douglas, G R; Dycaico, M J; Gorelick, N J; Provost, G S; Soussi, T

1997-01-01

245

Database of recent tsunami deposits  

USGS Publications Warehouse

This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

Peters, Robert; Jaffe, Bruce E.

2010-01-01

246

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems  

PubMed Central

The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased the number of microarray experiments to nine species. The increase of the number of expression data with multiple platforms could enhance the reliability of coexpression data. For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform. The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific null distribution. These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results. PMID:25392420

Okamura, Yasunobu; Aoki, Yuichi; Obayashi, Takeshi; Tadaka, Shu; Ito, Satoshi; Narise, Takafumi; Kinoshita, Kengo

2015-01-01

247

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.  

PubMed

The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased the number of microarray experiments to nine species. The increase of the number of expression data with multiple platforms could enhance the reliability of coexpression data. For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform. The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific null distribution. These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results. PMID:25392420

Okamura, Yasunobu; Aoki, Yuichi; Obayashi, Takeshi; Tadaka, Shu; Ito, Satoshi; Narise, Takafumi; Kinoshita, Kengo

2015-01-01

248

The AMMA database  

NASA Astrophysics Data System (ADS)

The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can concern local, satellite and model data. - Documentation: catalogue of all the available data and their metadata. These tools have been developed using standard and free languages and softwares: - Linux system with an Apache web server and a Tomcat application server; - J2EE tools : JSF and Struts frameworks, hibernate; - relational database management systems: PostgreSQL and MySQL; - OpenLDAP directory. In order to facilitate the access to the data by African scientists, the complete system has been mirrored at AGHRYMET Regional Centre in Niamey and is operational there since January 2009. Users can now access metadata and request data through one or the other of two equivalent portals: http://database.amma-international.org or http://amma.agrhymet.ne/amma-data.

Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

2010-05-01

249

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection  

PubMed Central

The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:23203983

Fernández-Suárez, Xosé M.; Galperin, Michael Y.

2013-01-01

250

Human cancer databases (Review)  

PubMed Central

Cancer is one of the four major non-communicable diseases (NCD), responsible for ~14.6% of all human deaths. Currently, there are >100 different known types of cancer and >500 genes involved in cancer. Ongoing research efforts have been focused on cancer etiology and therapy. As a result, there is an exponential growth of cancer-associated data from diverse resources, such as scientific publications, genome-wide association studies, gene expression experiments, gene-gene or protein-protein interaction data, enzymatic assays, epigenomics, immunomics and cytogenetics, stored in relevant repositories. These data are complex and heterogeneous, ranging from unprocessed, unstructured data in the form of raw sequences and polymorphisms to well-annotated, structured data. Consequently, the storage, mining, retrieval and analysis of these data in an efficient and meaningful manner pose a major challenge to biomedical investigators. In the current review, we present the central, publicly accessible databases that contain data pertinent to cancer, the resources available for delivering and analyzing information from these databases, as well as databases dedicated to specific types of cancer. Examples for this wealth of cancer-related information and bioinformatic tools have also been provided. PMID:25369839

PAVLOPOULOU, ATHANASIA; SPANDIDOS, DEMETRIOS A.; MICHALOPOULOS, IOANNIS

2015-01-01

251

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent  

PubMed Central

Background Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. Description FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. Conclusions FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance. PMID:24047532

2013-01-01

252

XMAn: a Homo sapiens mutated-peptide database for the MS analysis of cancerous cell states.  

PubMed

To enable the identification of mutated peptide sequences in complex biological samples, in this work, two novel cancer- and disease-related protein databases with mutation information collected from several public resources such as COSMIC, IARC P53, OMIM, and UniProtKB were developed. In-house developed Perl scripts were used to search and process the data and to translate each gene-level mutation into a mutated peptide sequence. The cancer and disease mutation databases comprise a total of 872,125 and 27,148 peptide entries from 25?642 and 2913 proteins, respectively. A description line for each entry provides the parent protein ID and name, the cDNA- and protein-level mutation site and type, the originating database, and the disease or cancer tissue type and corresponding hits. The two databases are FASTA-formatted to enable data retrieval by commonly used tandem MS search engines. While the largest number of mutations were encountered for the amino acids A/D/E/G/L/P/R/S, the global mutation profiles replicate closely the outcome of the 1000 Genomes Project aimed at cataloguing natural mutations in the human population. The affected proteins were primarily involved in transcription regulation, splicing, protein synthesis/folding/binding, redox/energy production, adhesion/motility, and to some extent in DNA damage repair and signaling. The applicability of the database to identifying the presence of mutated peptides was investigated with MCF-7 breast cancer cell extracts. PMID:25211293

Yang, Xu; Lazar, Iulia M

2014-12-01

253

TreeGenes: A Forest Tree Genome Database  

PubMed Central

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange. PMID:18725987

Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.; Neale, David B.

2008-01-01

254

CBS Databases  

NSDL National Science Digital Library

This major reference center for mycologists traces its existence back to 1903. Now an institute of the Royal Netherlands Academy of Arts and Sciences, CBS (Centraalbureau voor Schimmelcultures) continues to maintain and distribute one of the largest collections of living fungi in the world. With over 35,000 strains, "the collection contains representatives of virtually all fungal groups that can be cultured." Users can currently search six databases containing over 72,000 strains of fungi, yeasts, and bacteria held at CBS or other institutions. Each database offers several search options, such as by Species Name, Strain Number, or Properties of species/ strains. Search returns include Species, Variety, relevant Literature, Strain Number, Origin, History, and Form of Supply. The site also offers articles in HTML and .pdf format, information on current research themes and projects, strain ordering information, and an image gallery.

255

Trail Database  

NSDL National Science Digital Library

Something of a veteran by Internet standards, the Trail Database has been around since 1997 and, as such, now bills itself as the "world's largest hiking trail database." "Henk," the Dutch hiker responsible for this compendium, updates the site regularly and has included a wide variety of links to helpful material here. Users can search or browse the resources, which are arranged both under general topics, such as Knots or Equipment, and by country. Those planning European hikes will find the links off the front page to foot and mouth disease-related hiking restrictions useful (though we found some of these links to be broken). In all, an impressive collection of material. The site is available in Dutch or English.

256

Molecular Identification and Databases in Fusarium  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

257

Korea Barcode of Life Database System (KBOL)  

Microsoft Academic Search

A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using

Sungmin Kim; Chang-Bae Kim; Gi-Sik Min; Youngbae Suh; Jong Bhak; Taeha Woo; Hyeyoung Koo; Jun-Kil Choi; Mann Kyoon Shin; Jongwoo Jung; Kyo-Hong Song; Han-Il Ree; Ui Wook Hwang; Hae-Seok Eo; Joopil Kim; Seong Myeong Yoon; Hyun Soo Rho; Sa Heung Kim; Hang Lee; Mi-Sook Min; Jin Koo Kim; Chungja Sim; Yong-Jin Won; Jongwook Lee; Soowon Cho; Ji Eun Seo; Seunghwan Lee; Jun-Im Song; Ho-Yeon Han; Sook Shin; Sung Joon Song; Joong-Ki Park; Keeseon S. Eom; Jung Hee Park; Won Kim

2012-01-01

258

Korea Barcode of Life Database System (KBOL)  

Microsoft Academic Search

A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using

Sungmin Kim; Chang-Bae Kim; Gi-Sik Min; Youngbae Suh; Jong Bhak; Taeha Woo; Hyeyoung Koo; Jun-Kil Choi; Mann Kyoon Shin; Jongwoo Jung; Kyo-Hong Song; Han-Il Ree; Ui Wook Hwang; Hae-Seok Eo; Joopil Kim; Seong Myeong Yoon; Hyun Soo Rho; Sa Heung Kim; Hang Lee; Mi-Sook Min; Jin Koo Kim; Chungja Sim; Yong-Jin Won; Jongwook Lee; Soowon Cho; Ji Eun Seo; Seunghwan Lee; Jun-Im Song; Ho-Yeon Han; Sook Shin; Sung Joon Song; Joong-Ki Park; Keeseon S. Eom; Jung Hee Park; Won Kim

2011-01-01

259

ARTI Refrigerant Database  

SciTech Connect

The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

Calm, J.M.

1992-11-09

260

Physiological Parameters Database for PBPK Modeling (External Review Draft)  

EPA Science Inventory

EPA released for public comment a physiological parameters database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence. It also contains similar data for an...

261

The IPD and IMGT/HLA database: allele variant databases  

PubMed Central

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities. PMID:25414341

Robinson, James; Halliwell, Jason A.; Hayhurst, James D.; Flicek, Paul; Parham, Peter; Marsh, Steven G. E.

2015-01-01

262

Comparison of DNA Sequences with Protein Sequences  

Microsoft Academic Search

The FASTA package of sequence comparison programs has been expanded to include FASTX and FASTY, which compare a DNA sequence to a protein sequence database, translating the DNA sequence in three frames and aligning the translated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts. Also new are TFASTX and TFASTY, which compare a protein sequence

William R. Pearson; Todd Wood; Zheng Zhang; Webb Miller

1997-01-01

263

Working on the public Human Genome Project, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>The project>players>money Threatening their funding Craig Venter speaks about the public sector's reaction to his plans to sequence the genome at a private company, Celera Genomics.

2008-10-06

264

A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity  

EPA Science Inventory

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

265

Publication Bias in Antipsychotic Trials: An Analysis of Efficacy Comparing the Published Literature to the US Food and Drug Administration Database  

PubMed Central

Background Publication bias compromises the validity of evidence-based medicine, yet a growing body of research shows that this problem is widespread. Efficacy data from drug regulatory agencies, e.g., the US Food and Drug Administration (FDA), can serve as a benchmark or control against which data in journal articles can be checked. Thus one may determine whether publication bias is present and quantify the extent to which it inflates apparent drug efficacy. Methods and Findings FDA Drug Approval Packages for eight second-generation antipsychotics—aripiprazole, iloperidone, olanzapine, paliperidone, quetiapine, risperidone, risperidone long-acting injection (risperidone LAI), and ziprasidone—were used to identify a cohort of 24 FDA-registered premarketing trials. The results of these trials according to the FDA were compared with the results conveyed in corresponding journal articles. The relationship between study outcome and publication status was examined, and effect sizes derived from the two data sources were compared. Among the 24 FDA-registered trials, four (17%) were unpublished. Of these, three failed to show that the study drug had a statistical advantage over placebo, and one showed the study drug was statistically inferior to the active comparator. Among the 20 published trials, the five that were not positive, according to the FDA, showed some evidence of outcome reporting bias. However, the association between trial outcome and publication status did not reach statistical significance. Further, the apparent increase in the effect size point estimate due to publication bias was modest (8%) and not statistically significant. On the other hand, the effect size for unpublished trials (0.23, 95% confidence interval 0.07 to 0.39) was less than half that for the published trials (0.47, 95% confidence interval 0.40 to 0.54), a difference that was significant. Conclusions The magnitude of publication bias found for antipsychotics was less than that found previously for antidepressants, possibly because antipsychotics demonstrate superiority to placebo more consistently. Without increased access to regulatory agency data, publication bias will continue to blur distinctions between effective and ineffective drugs. Please see later in the article for the Editors' Summary PMID:22448149

Turner, Erick H.; Knoepflmacher, Daniel; Shapley, Lee

2012-01-01

266

Generation and Analysis of a Large-Scale Expressed Sequence Tag Database from a Full-Length Enriched cDNA Library of Developing Leaves of Gossypium hirsutum L  

PubMed Central

Background Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. Methodology/Principal Findings In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. Conclusions/Significance These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species. PMID:24146870

Pang, Chaoyou; Fan, Shuli; Song, Meizhen; Yu, Shuxun

2013-01-01

267

Open Geoscience Database  

NASA Astrophysics Data System (ADS)

Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data treatment could be conducted in other programs after extraction the filtered data into *.csv file. It makes the database understandable for non-experts. The database employs open data format (*.csv) and wide spread tools: PHP as the program language, MySQL as database management system, JavaScript for interaction with GoogleMaps and JQueryUI for create user interface. The database is multilingual: there are association tables, which connect with elements of the database. In total the development required about 150 hours. The database still has several problems. The main problem is the reliability of the data. Actually it needs an expert system for estimation the reliability, but the elaboration of such a system would take more resources than the database itself. The second problem is the problem of stream selection - how to select the stations that are connected with each other (for example, belong to one water stream) and indicate their sequence. Currently the interface is English and Russian. However it can be easily translated to your language. But some problems we decided. For example problem "the problem of the same station" (sometimes the distance between stations is smaller, than the error of position): when you adding new station to the database our application automatically find station near this place. Also we decided problem of object and parameter type (how to regard "EC" and "electrical conductivity" as the same parameter). This problem has been solved using "associative tables". If you would like to see the interface on your language, just contact us. We should send you the list of terms and phrases for translation on your language. The main advantage of the database is that it is totally open: everybody can see, extract the data from the database and use them for non-commercial purposes with no charge. Registered users can contribute to the database without getting paid. We hope, that it will be widely used first of all for education purposes, but professional scientists could use it also.

Bashev, A.

2012-04-01

268

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants  

PubMed Central

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-01-01

269

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.  

PubMed

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

270

Transboundary Freshwater Dispute Database  

NSDL National Science Digital Library

The database includes 150 water related treaties and 39 US compacts. The International Treaties and Compacts section is searchable by nation, basin, issues, conflict resolution mechanisms, non-water linkages, and date. US Compacts are searchable by state, basin, focus and date. For all treaties or compacts there is a summary of the agreement, the parties involved, allocations if applicable and other information pertinent to a specific agreement. There is also information available on indigenous approaches to water conflict resolution, a digitized inventory of the world's river basins with data about those basins, and a bibliography featuring publications about transboundary freshwater dispute resolution.

271

Missionary Periodicals Database  

NSDL National Science Digital Library

Hosted by the Yale Divinity School and created by the Currents in World Christianity Center at the University of Cambridge, this site is an amazing resource for anyone studying British missionary movements, religion, or the British empire. Visitors can browse the database by region or periodical title, or conduct a keyword search. Initial returns include title, issuing body, denomination, place, and dates of publication. Full entries include publisher, volume numbers, frequency, circulation, price, region of work, features, and some comments. Scholars who study these materials will undoubtedly make great use of this site.

272

Lighthouse Explorer Database  

NSDL National Science Digital Library

Spotted by ResearchBuzz, this site from the Lighthouse Depot, a "virtual community" (and store) for lighthouse enthusiasts, contains a database with information on over 1,300 lighthouses around the world. Visitors may browse the listings alphabetically, by category, by state or country, or search by keyword. Entries include name, location, supervising organization, contact information, email and Website when available, and in some cases a photo. Other useful information is also provided when available, such as the dates the lighthouse was built and operational, whether or not it is open to the public, and driving directions.

273

NIST Scientific and Technical Databases  

NSDL National Science Digital Library

NIST has long been developing and compiling benchmark data for the properties of important substances, classes of substances and systems. It's data collections, data prediction methods and models meet high priority industrial and national needs. This list of databases contribute to U.S. industry's productivity and competitiveness and improve public health, safety and environmental quality.

274

REFEREE: BIBLIOGRAPHIC DATABASE MANAGER, DOCUMENTATION  

EPA Science Inventory

The publication is the user's manual for 3.xx releases of REFEREE, a general-purpose bibliographic database management program for IBM-compatible microcomputers. The REFEREE software also is available from NTIS. The manual has two main sections--Quick Tour and References Guide--a...

275

mtDNA Variation and Analysis Using MITOMAP and MITOMASTER  

PubMed Central

The MITOMAP database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The MITOMAP protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within MITOMAP is the powerful sequence analysis tool for human mitochondrial DNA, MITOMASTER. The MITOMASTER protocol gives step-by-step instructions showing how to submit sequences to identify nucleotide variants relative to the rCRS, to determine the haplogroup, and to view species conservation. User-supplied sequences, GenBank identifiers and single nucleotide variants may be analyzed. PMID:25489354

Lott, Marie T.; Leipzig, Jeremy N.; Derbeneva, Olga; Xie, H. Michael; Chalkia, Dimitra; Sarmady, Mahdi; Procaccio, Vincent; Wallace, Douglas C.

2014-01-01

276

Re-identification of DNA through an automated linkage process.  

PubMed Central

This work demonstrates how seemingly anonymous DNA database entries can be related to publicly available health information to uniquely and specifically identify the persons who are the subjects of the information even though the DNA information contains no accompanying explicit identifiers such as name, address, or Social Security number and contains no additional fields of personal information. The software program, REID (Re-Identification of DNA), iteratively uncovers unique occurrences in visit-disease patterns across data collections that reveal inferences about the identities of the patients who are the subject of the DNA. Using real-world data, REID established identifiable linkages in 33-100% of the 10,886 cases explicitly surveyed over 8 gene-based diseases. PMID:11825223

Malin, B.; Sweeney, L.

2001-01-01

277

NICMOS HISTORY DATABASE AND April 10, 1998  

E-print Network

1 NICMOS HISTORY DATABASE AND WEB TOOLS C. Tullos April 10, 1998 ABSTRACT The history of NICMOS on the World Wide Web. The history tool which allows queries on the data, is available to the public. 1. The Database and Data A convenient way of keeping a history of some of the NICMOS instrument parameters

Sirianni, Marco

278

Correlates of Access to Business Research Databases  

ERIC Educational Resources Information Center

This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

Gottfried, John C.

2010-01-01

279

An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data.  

PubMed

With 1383 tandem mass spectra derived from 120 individual protein spots separated by the two-dimensional (2-D) gel electrophoresis of protein samples from three different species, comparative analyses were performed by searching the Expressed Sequence Tag (EST) database (DB) and the NCBI non-redundant (nr) DB of green plants, respectively, which uses the Mascot search engine to establish a statistical basis. It was confirmed that the former could identify more peptides manually validated by de novo sequencing (DNS) from fewer species in more closely phylogenetic relationships than the latter in a statistically significant manner. Our data demonstrated that correct peptide identifications were given low Mascot scores (e.g. 6-14) and incorrect peptide identifications were given high Mascot scores (e.g. 68-83). Our data also showed that the current evaluation approaches to protein assignments are unsatisfactory because a few 'false-positive' proteins are recognized and several 'false-negative' proteins are rescued by manual validation. PMID:16941525

Huang, Mei; Chen, Tong; Chan, ZhuLong

2006-01-01

280

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

Cain, J.M. [Calm (James M.), Great Falls, VA (United States)

1993-04-30

281

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M.

1997-02-01

282

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

1998-08-01

283

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates. Citations in this report are divided into the following topics: thermophysical properties; materials compatibility; lubricants and tribology; application data; safety; test and analysis methods; impacts; regulatory actions; substitute refrigerants; identification; absorption and adsorption; research programs; and miscellaneous documents. Information is also presented on ordering instructions for the computerized version.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)] [Calm (James M.), Great Falls, VA (United States)

1996-04-15

284

Lost Art Internet Database  

NSDL National Science Digital Library

Launched on April 10, the Lost Art Internet Database is a collaborative project of the Federal Government of Germany and its Federal States ("Lander"). The site "registers cultural goods which were transported or stolen because of persecution, especially of Jewish citizens, as a result of World War II or as a result of National Socialism." At the site users can currently conduct simple or advanced searches of two areas of the database: Public Losses and Remaining Stock CCP. Alternatively, users can search both simultaneously via the Global Search function. Search returns for the former include title, type of object, whether or not it was a war loss, destroyed, or restituted, and a contact for further information. Those for the latter include title, artist, material, measures, purchase, borrower, and inventory number. Background and additional information on the project as a whole and the currently available content are provided. Please note that the site is still under extensive construction and more content is forthcoming. Additions planned for the near future include a "Fremdbesitz" area of the database that will list objects, regardless of their location, that are not in the owner's hands or are without provenance, and an expanded Other Countries section that may include data from other countries.

285

Evaluation of the database on mutant frequencies and DNA sequence alterations of vermilion mutations induced in germ cells of Drosophila shows the importance of a neutral mutation detection system.  

PubMed

The vermilion gene in Drosophila has extensively been used for the molecular analysis of mutations induced by chemicals in germ cells in vivo. The gene is located on the X-chromosome and is a useful target for the study of mutagenesis since all types of mutations are generated. We have critically evaluated this system with respect to sensitivity for mutation induction and selectivity for different types of mutations, using a database of more than 600 vermilion mutants induced in postmeiotic male germ cells by 18 mutagens. From most of these mutants the mutation has been analysed. These data showed 336 base substitutions, 96 intra-locus DNA rearrangements and 78 multi-locus deletions (MLD). Mutants containing a MLD were either heterozygous sterile or homozygous and hemizygous lethal. The distribution of both basepair (bp) changes and intra-locus rearrangements over the coding region of the vermilion gene was uniform with no preferences concerning 5' or 3' regions, certain exons, splice sites, specific amino acid changes or nonsense mutations. Possible hotspots for base substitutions seem to be related to the type of DNA damage rather than to the vermilion system. Gene mutations other than bp changes were examined on sequence characteristics flanking the deletion breakpoints. Induction frequencies of vermilion mosaic mutants were, in general, higher than those of vermilion complete mutants, suggesting that persistent lesions are the main contributors to the molecular spectra. Comparison of induction frequencies of vermilion mutants and sex-linked recessive lethal (SLRL) mutants for the 18 mutagens showed that the sensitivity of the vermilion gene against a mutagenic insult is representative for genes located on the X-chromosome. The effect of nucleotide excision repair (NER) on the formation of SLRL mutants correlated with an increase of transversions in the vermilion spectra under NER deficient conditions. Furthermore, the clastogenic potency of the mutagens, i.e., the efficiency to induce chromosomal-losses vs. SLRL forward mutations, shows a positive correlation with the percentage of DNA deletions in the molecular spectra of vermilion mutants. PMID:10656485

Nivard, M J; Aguirrezabalaga, I; Ballering, L A; Pastink, A; Sierra, L M; Vogel, E W

1999-12-16

286

Algaline Database  

NSDL National Science Digital Library

Maintained by the Finnish Institute of Marine Research and several other institutions, the Algaline Database offers updated reports on the conditions of phytoplankton and related parameters in the Baltic Sea. The reports, which vary in length and detail (though most are brief), summarize measurements of Oxygen, Salinity, Temperature, Nutrients, Harmful substances, Plankton, Zooplankton, Benthic Animals, Flow, and Other measurements. In addition, the Maps and Figures section offers numerous color images (including satellite) of Baltic Sea conditions and marine organisms. To access reports by geographic subregion of the Baltic, head to the Reports section. Finally, the Latest News section keeps researchers abreast of changing conditions (e.g., algal blooms) and research cruises in the Baltic. For researchers or anyone else wanting in-depth information on a host of ecological parameters for the Baltic Sea, this is an excellent reference site.

287

USDA Forest Service Southern Research Station: Publications  

NSDL National Science Digital Library

This database contains publications in support of this group\\'s mission to create the science and technology needed to sustain and enhance southern forest ecosystems and the benefits they provide. The database can be searched by author, title, keyword, date range, and publication origin; publication number; and by the most recent publications added to the database. There are also online versions of Compass, a publication catalog of research products from scientists at SRS.

288

DNA secret writing techniques  

Microsoft Academic Search

The paper presents the principles of bio molecular computation (BMC) and several algorithms for DNA (deoxyribonucleic acid) steganography and cryptography: One-Time-Pad (OTP), DNA XOR OTP and DNA chromosomes indexing. It represents a synthesis of our work in the field, sustained by former referred publications. Experimental results obtained using Matlab Bioinformatics Toolbox and conclusions are ending the work.

Monica BORDA; Olga TORNEA

2010-01-01

289

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.  

PubMed

The report that exogenous plant miRNAs are able to cross the mammalian gastrointestinal tract and exert gene-regulation mechanism in mammalian tissues has yielded a lot of controversy, both in the public press and the scientific literature. Despite the initial enthusiasm, reproducibility of these results was recently questioned by several authors. To analyze the causes of this unease, we searched for diet-derived miRNAs in deep-sequencing libraries performed by ourselves and others. We found variable amounts of plant miRNAs in publicly available small RNA-seq data sets of human tissues. In human spermatozoa, exogenous RNAs reached extreme, biologically meaningless levels. On the contrary, plant miRNAs were not detected in our sequencing of human sperm cells, which was performed in the absence of any known sources of plant contamination. We designed an experiment to show that cross-contamination during library preparation is a source of exogenous RNAs. These contamination-derived exogenous sequences even resisted oxidation with sodium periodate. To test the assumption that diet-derived miRNAs were actually contamination-derived, we sought in the literature for previous sequencing reports performed by the same group which reported the initial finding. We analyzed the spectra of plant miRNAs in a small RNA sequencing study performed in amphioxus by this group in 2009 and we found a very strong correlation with the plant miRNAs which they later reported in human sera. Even though contamination with exogenous sequences may be easy to detect, cross-contamination between samples from the same organism can go completely unnoticed, possibly affecting conclusions derived from NGS transcriptomics. PMID:24729469

Tosar, Juan Pablo; Rovira, Carlos; Naya, Hugo; Cayota, Alfonso

2014-06-01

290

NBC update: The addition of viral and fungal databases to the Naďve Bayes classification tool  

PubMed Central

Background Classifying the fungal and viral content of a sample is an important component of analyzing microbial communities in environmental media. Therefore, a method to classify any fragment from these organisms' DNA should be implemented. Results We update the näive Bayes classification (NBC) tool to classify reads originating from viral and fungal organisms. NBC classifies a fungal dataset similarly to Basic Local Alignment Search Tool (BLAST) and the Ribosomal Database Project (RDP) classifier. We also show NBC's similarities and differences to RDP on a fungal large subunit (LSU) ribosomal DNA dataset. For viruses in the training database, strain classification accuracy is 98%, while for those reads originating from sequences not in the database, the order-level accuracy is 78%, where order indicates the taxonomic level in the tree of life. Conclusions In addition to being competitive to other classifiers available, NBC has the potential to handle reads originating from any location in the genome. We recommend using the Bacteria/Archaea, Fungal, and Virus databases separately due to algorithmic biases towards long genomes. The tool is publicly available at: http://nbc.ece.drexel.edu. PMID:22293603

2012-01-01

291

DMTB: the magnetotactic bacteria database  

NASA Astrophysics Data System (ADS)

Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

Pan, Y.; Lin, W.

2012-12-01

292

Environment Australia's Online Image Database  

NSDL National Science Digital Library

Environment Australia -- Australia's Department of Environment and Heritage -- has made its extensive collection of photographs freely available for non-commercial use. Researchers and students in the environmental sciences may find this collection of well-composed, high-quality images a useful resource for presentations and publications. Users may easily search the database by keyword, general subject, and/or geographic area. Search results yield a table of thumbnail photos together with summary information for each image. Before publishing an image from the database, users must first contact Environment Australia (via provided Web form).

293

CD-ROM-aided Databases  

NASA Astrophysics Data System (ADS)

CD-ROM has rapidly evolved as a new information medium with large capacity, In the U.S. it is predicted that it will become two hundred billion yen market in three years, and thus CD-ROM is strategic target of database industry. Here in Japan the movement toward its commercialization has been active since this year. Shall CD-ROM bussiness ever conquer information market as an on-disk database or electronic publication? Referring to some cases of the applications in the U.S. the author views marketability and the future trend of this new optical disk medium.

Masuyama, Keiichi

294

Overlap in Bibliographic Databases.  

ERIC Educational Resources Information Center

Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases.…

Hood, William W.; Wilson, Concepcion S.

2003-01-01

295

Searching and Indexing Genomic Databases via Kernelization  

PubMed Central

The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper, we survey the 20-year history of this idea and discuss its relation to kernelization in parameterized complexity. PMID:25710001

Gagie, Travis; Puglisi, Simon J.

2015-01-01

296

Searching and Indexing Genomic Databases via Kernelization.  

PubMed

The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper, we survey the 20-year history of this idea and discuss its relation to kernelization in parameterized complexity. PMID:25710001

Gagie, Travis; Puglisi, Simon J

2015-01-01

297

Face Verification Competition on the XM2VTS Database  

Microsoft Academic Search

In the year 2000 a competition was organised to collect face verification results on an identical, publicly available data set us- ing a standard evaluation protocol. The database used was the Xm2vts database along with the Lausanne protocol (14). Four different institu- tions submitted results on the database which were subsequently pub- lished in (13). Three years later, a second

Kieron Messer; Josef Kittler; Mohammad Sadeghi; Sébastien Marcel; Christine Marcel; Samy Bengio; Fabien Cardinaux; Conrad Sanderson; Jacek Czyz; Luc Vandendorpe; Sanun Srisuk; Maria Petrou; Werasak Kurutach; Alexander Kadyrov; Roberto Paredes; Burcu Kepenekci; F. Boray Tek; Gozde Bozdagi Akar; Farzin Deravi; Nick Mavity

2003-01-01

298

Marginal public health gain of screening for colorectal cancer: modelling study, based on WHO and national databases in the Nordic countries  

PubMed Central

Aims To estimate the potential gain of national screening programmes for colorectal cancer (CRC) by stool occult blood testing in the Nordic countries, with comparative reference to the burden of other causes of premature death. Methods Implementation of national screening programmes for CRC was modelled among people 55–74 years in accordance with the 2011 Cochrane review of biannual screening, using the faecal occult blood test (FOBT) for 10 years, resulting in 15% relative risk reduction in CRC deaths among all those invited [intention-to-treat; relative risk 0.85; confidence interval (CI) 0.78 to 0.92]. Our calculations are based on the World Health Organization and national databanks on death causes (ICD-10) and the mid-year number of inhabitants in the target group. For Finland, Denmark, Norway and Sweden, we used data for 2009. For Iceland, due to the population's small size, we calculated mean mortality for the period 2005–2009. Results Invitation to a CRC screening programme for 10 years could influence 0.5–0.9% (95%CI 0.4–1.2) of all deaths in the age group 65–74 years. Among the remaining 99% of premature deaths, around 50% were caused by lung cancer, other lung diseases, cardiovascular diseases and accidents, with some national variations. Conclusions and implications Establishment of a screening programme for CRC for people aged 55–74 can be expected to affect only a minor proportion of all premature deaths in the Nordic setting. From a public health perspective, prioritizing preventive strategies targeting more prevalent causes of premature death may be a superior approach. PMID:22519671

Sigurdsson, Johann A; Getz, Linn; Sjönell, Göran; Vainiomäki, Paula; Brodersen, John

2013-01-01

299

ASMENET Jobs Database  

NSDL National Science Digital Library

The American Society of Mechanical Engineers offers this searchable and browsable (see database search tip) database of Mechanical Engineering related jobs. The database can be searched by location, title, company, or job responsibilities.

1998-01-01

300

Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead.  

PubMed

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead. PMID:24118947

Joly, Simon; Davies, T Jonathan; Archambault, Annie; Bruneau, Anne; Derry, Alison; Kembel, Steven W; Peres-Neto, Pedro; Vamosi, Jana; Wheeler, Terry A

2014-03-01

301

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa  

PubMed Central

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. PMID:22123747

D'Onorio de Meo, Paolo; D'Antonio, Mattia; Griggio, Francesca; Lupi, Renato; Borsani, Massimiliano; Pavesi, Giulio; Castrignanň, Tiziana; Pesole, Graziano; Gissi, Carmela

2012-01-01

302

Approaching Analysis of EU IST Projects Database  

Microsoft Academic Search

We present the first results of the analysis of publicly available EU IST project descriptions. The database was automatically built from the publicly available information on the Web and organized to enable further analysis. We have used Text Mining methods to group the projects according to their content and the institutions participating in the projects. Two systems were developed, the

Marko Grobelnik

303

CEBAF Large Acceptance Spectrometer (CLAS) Physics Database  

DOE Data Explorer

A username and password are required to access and search the entire database. However, the Overview page provides links to detailed data pages for each of the experiments available for public access. There are many experiments with data that the public can freely access.

304

National Residential Efficiency Measures Database  

DOE Data Explorer

The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Software developers who require residential retrofit performance and cost data for applications that evaluate residential efficiency measures are the primary audience for this database. In addition, home performance contractors and manufacturers of residential materials and equipment may find this information useful. The database offers the following types of retrofit measures: 1) Appliances, 2) Domestic Hot Water, 3) Enclosure, 4) Heating, Ventilating, and Air Conditioning (HVAC), 5) Lighting, 6) Miscellaneous.

305

National Geologic Map Database  

NSDL National Science Digital Library

The National Geologic Map Database (NGMDB) is an Internet-based system for query and retrieval of earth-science map information, created as a collaborative effort between the USGS and the Association of American State Geologists. Its functions include providing a catalog of available map information; a data repository; and a source for general information on the nature and intended uses of the various types of earth-science information. The map catalog is a comprehensive, searchable catalog of all geoscience maps of the United States, in paper or digital format. It includes maps published in geological survey formal series and open-file series, maps in books, theses and dissertations, maps published by park associations, scientific societies, and other agencies, as well as publications that do not contain a map but instead provide a geological description of an area (for example, a state park). The geologic-names lexicon (GEOLEX) is a search tool for lithologic and geochronologic unit names. It now contains roughly 90% of the geologic names found in the most recent listing of USGS-approved geologic names. Current mapping activities at 1:24,000- and 1:100,000-scale are listed in the Geologic Mapping in Progress Database. Information on how to find topographic maps and list of geology-related links is also available.

1997-01-01

306

Mouse phenome database.  

PubMed

The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

Grubb, Stephen C; Bult, Carol J; Bogue, Molly A

2014-01-01

307

Alcohol Studies Database  

NSDL National Science Digital Library

Since 1987, staff members at the Rutgers University Center of Alcohol Studies have been collecting citations of documents related to alcohol. Today, they have over 80,000 citations and much of the material is related to research and professional materials that deal with the subject. Additionally, the database contains a small collection of educational and prevention materials designed for use by educators, parents, and public health workers. The site is maintained by the Scholarly Communication Center, the Center of Alcohol Studies, and the Rutgers University Libraries. Visitors to the site can search by subject, or perform a more advanced search as well. The site also includes a "Help" area, which includes information on limiting searches, links to full text, and suggestions on using Boolean techniques.

308

Mouse Phenome Database  

PubMed Central

The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

Grubb, Stephen C.; Bult, Carol J.; Bogue, Molly A.

2014-01-01

309

Interactive bibliographical database on color  

NASA Astrophysics Data System (ADS)

The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

Caivano, Jose L.

2002-06-01

310

Three Decades of Recombinant DNA.  

ERIC Educational Resources Information Center

Discusses highlights in the development of genetic engineering, examining techniques with recombinant DNA, legal and ethical issues, GenBank (a national database of nucleic acid sequences), and other topics. (JN)

Palmer, Jackie

1985-01-01

311

Creating a Serial Database Using Subscription Agency Files  

Microsoft Academic Search

Subscription agency invoice files on diskette can be transferred into standard microcomputer database management packages to provide libraries with a fast low-cost serials database useful for various public or technical service functions and for management decision-making. Specific procedures are detailed for producing such a database using EBSCO Subscription Services invoice diskettes and the PC-File III and dBASE III PLUS database

Susan A. Cady

1988-01-01

312

Saudi Arabian National Center for Science and Technology (SANCST) Database.  

ERIC Educational Resources Information Center

Subject areas covered by publications in database of Saudi Arabian National Center for Science and Technology are enumerated, noting Saudi contribution: total number of publications in individual subject areas, number of publications for each area and year, and publication trends (1960-1982). Scientific and technological activities in Saudi Arabia…

Manzoor, Suhail

1985-01-01

313

Curation accuracy of model organism databases  

PubMed Central

Manual extraction of information from the biomedical literature—or biocuration—is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

Keseler, Ingrid M.; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y.; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C.; Mladinich, Katherine M.; Chow, Edmond D.; Sherlock, Gavin; Karp, Peter D.

2014-01-01

314

Curation accuracy of model organism databases.  

PubMed

Manual extraction of information from the biomedical literature-or biocuration-is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

Keseler, Ingrid M; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C; Mladinich, Katherine M; Chow, Edmond D; Sherlock, Gavin; Karp, Peter D

2014-01-01

315

The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins.  

PubMed

The Chloroplast Function Database has so far offered phenotype information on mutants of the nuclear-encoded chloroplast proteins in Arabidopsis that pertains to >200 phenotypic data sets that were obtained from 1,722 transposon- or T-DNA-tagged lines. Here, we present the development of the second version of the database, which is named the Chloroplast Function Database II and was redesigned to increase the number of mutant characters and new user-friendly tools for data mining and integration. The upgraded database offers information on genome-wide mutant screens for any visible phenotype against 2,495 tagged lines to create a comprehensive homozygous mutant collection. The collection consists of 147 lines with seedling phenotypes and 185 lines for which we could not obtain homozygotes, as well as 1,740 homozygotes with wild-type phenotypes. Besides providing basic information about primer lists that were used for the PCR genotyping of T-DNA-tagged lines and explanations about the preparation of homozygous mutants and phenotype screening, the database includes access to a link between the gene locus and existing publicly available databases. This gives users access to a combined pool of data, enabling them to gain valuable insights into biological processes. In addition, high-resolution images of plastid morphologies of mutants with seedling-specific chloroplast defects as observed with transmission electron microscopy (TEM) are available in the current database. This database is used to compare the phenotypes of visually identifiable mutants with their plastid ultrastructures and to evaluate their potential significance from characteristic patterns of plastid morphology in vivo. Thus, the Chloroplast Function Database II is a useful and comprehensive information resource that can help researchers to connect individual Arabidopsis genes to plastid functions on the basis of phenotype analysis of our tagged mutant collection. It can be freely accessed at http://rarge.psc.riken.jp/chloroplast/. PMID:23230006

Myouga, Fumiyoshi; Akiyama, Kenji; Tomonaga, Yumi; Kato, Aya; Sato, Yuka; Kobayashi, Megumi; Nagata, Noriko; Sakurai, Tetsuya; Shinozaki, Kazuo

2013-02-01

316

Database Encryption Luc Bouganim  

E-print Network

Database Encryption Luc Bouganim INRIA Rocquencourt Le Chesnay, FRANCE Luc.Bouganim@inria.fr Yanli security, Data confidentiality, Hardware Security Module Definition Database encryption refers to the use of encryption techniques to transform a plain text database into a (partially) encrypted database, thus making

317

Databases: Beyond the Basics.  

ERIC Educational Resources Information Center

This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

Whittaker, Robert

318

Database Management Certificate Program  

E-print Network

Database Management Certificate Program DATABASE TECHNOLOGIES 13 Today, organizations in every to obtain general data analysis and management skills or apply both Oracle and Microsoft SQL Server database capabilities of relational databases in conjunction with the new "Big Data" management frameworks for data

Rose, Michael R.

319

Reflective Database Access Control  

ERIC Educational Resources Information Center

"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

Olson, Lars E.

2009-01-01

320

The UCSC Genome Browser database: 2015 update  

PubMed Central

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), ‘mined the web’ for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

Rosenbloom, Kate R.; Armstrong, Joel; Barber, Galt P.; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R.; Fujita, Pauline A.; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A.; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S.; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin H.; Miga, Karen H.; Nguyen, Ngan; Paten, Benedict; Raney, Brian J.; Smit, Arian F. A.; Speir, Matthew L.; Zweig, Ann S.; Haussler, David; Kuhn, Robert M.; Kent, W. James

2015-01-01

321

The UCSC Genome Browser database: 2015 update.  

PubMed

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. PMID:25428374

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T; Li, Chin H; Miga, Karen H; Nguyen, Ngan; Paten, Benedict; Raney, Brian J; Smit, Arian F A; Speir, Matthew L; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

2015-01-01

322

Human Mitochondrial Protein Database  

National Institute of Standards and Technology Data Gateway

SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

323

LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study  

PubMed Central

Besides its important significance in plant taxonomy and phylogeny, sacred lotus (Nelumbo nucifera Gaertn.) might also hold the key to the secrets of aging, which attracts crescent attentions from researchers all over the world. The genetic or molecular studies on this species depend on its genome information. In 2013, two publications reported the sequencing of its full genome, based on which we constructed a database named as LOTUS-DB. It will provide comprehensive information on the annotation, gene function and expression for the sacred lotus. The information will facilitate users to efficiently query and browse genes, graphically visualize genome and download a variety of complex data information on genome DNA, coding sequence (CDS), transcripts or peptide sequences, promoters and markers. It will accelerate researches on gene cloning, functional identification of sacred lotus, and hence promote the studies on this species and plant genomics as well. Database URL: http://lotus-db.wbgcas.cn. PMID:25819075

Wang, Kun; Deng, Jiao; Damaris, Rebecca Njeri; Yang, Mei; Xu, Liming; Yang, Pingfang

2015-01-01

324

Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair  

Microsoft Academic Search

Based on the crystal structure of human DNA ligase I complexed with nicked DNA, computer-aided drug design was used to identify compounds in a database of 1.5 million commercially available low molecular weight chemicals that were predicted to bind to a DNA-binding pocket within the DNA-binding domain of DNA ligase I, thereby inhibiting DNA joining. Ten of 192 candidates specifically

Xi Chen; Shijun Zhong; Xiao Zhu; Barbara Dziegielewska; Tom Ellenberger; Gerald M. Wilson; Alexander D. MacKerell; Alan E. Tomkinson

2008-01-01

325

Job Announcement Development Database Coordinator  

E-print Network

Database Coordinator. The Development Database Coordinator is the principle manager of the donor database. The Database Coordinator manages and maintains Holden's / Cleveland Botanical Garden's confidential donor on advances in database management software; provides administrative support for the development department

Isaacs, Rufus

326

Privacy-Preserving Matching of DNA Profiles Fons Bruekers1  

E-print Network

Privacy-Preserving Matching of DNA Profiles Fons Bruekers1 , Stefan Katzenbeisser1,2 , Klaus a commodity. Most western governments keep databases with DNA profiles of criminal offenders and suspects profiles; the British authorities alone maintain a database containing DNA samples of more than five per

327

Fusarium identification databases, present and future  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA-sequence based identification of fungi is now in wide practice. For a community molecular identification tool to be effective, it must be based on an appropriately informative locus or set of loci, technology that is broadly available, and most importantly, connected to a definitive database. ...

328

The Organelle Genome Database Project (GOBASE).  

PubMed Central

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data. PMID:9399818

Korab-Laskowska, M; Rioux, P; Brossard, N; Littlejohn, T G; Gray, M W; Lang, B F; Burger, G

1998-01-01

329

DNA Barcoding for Species Assignment: The Case of Mediterranean Marine Fishes  

PubMed Central

Background DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%–18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity. PMID:25222272

Landi, Monica; Dimech, Mark; Arculeo, Marco; Biondo, Girolama; Martins, Rogelia; Carneiro, Miguel; Carvalho, Gary Robert; Brutto, Sabrina Lo; Costa, Filipe O.

2014-01-01

330

DNA Sequencing apparatus  

DOEpatents

An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1992-01-01

331

Silicon Valley Companies Database (SV150)  

NSDL National Science Digital Library

Created by Mercury Center, the online service of the San Jose Mercury News, this database offers financial information and company background for the 150 largest publicly traded companies in Silicon Valley. Silicon Valley is defined as the cities of Santa Cruz and Santa Clara, as well as the southern sections of San Mateo and Alameda counties. The database is searchable by company name, stock symbol, 1997 sales, industry type, product, and location. Clear, detailed instructions will help users best use the database. The search results link to company homepages and charted stock prices.

332

University of Washington: Database Research Group  

NSDL National Science Digital Library

The University of Washington's Database Research Group â??is focused on broadening the scope of database and data management techniques beyond their traditional scope.â?ť Its work focuses on databases and the Web, XML, data management for ubiquitous computing, data integration, and data mining. For example, the Mangrove project seeks to facilitate the move to the semantic Web by creating â??an environment in which users are motivated to create semantic content because of the existence of useful semantic services.â?ť The various projects are described on this website along with related publications, which are available to download.

333

YMDB: the Yeast Metabolome Database.  

PubMed

The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S

2012-01-01

334

Genotype-based databases for variants causing rare diseases.  

PubMed

Inherited diseases are the result of DNA sequence changes. In recessive diseases, the clinical phenotype results from the combined functional effects of variants in both copies of the gene. In some diseases there is often considerable variability of clinical presentation or disease severity, which may be predicted by the genotype. Additional effects may be triggered by environmental factors, as well as genetic modifiers which could be nucleotide polymorphisms in related genes, e.g. maternal ApoE or ABCA1 genotypes which may have an influence on the phenotype of SLOS individuals. Here we report the establishment of genotype variation databases for various rare diseases which provide individual clinical phenotypes associated with genotypes and include data about possible genetic modifiers. These databases aim to be an easy public access to information on rare and private variants with clinical data, which will facilitate the interpretation of genetic variants. The created databases include ACAD8 (isobutyryl-CoA dehydrogenase deficiency (IBD)), ACADSB (short-chain acyl-CoA dehydrogenase (SCAD) deficiency), AUH (3-methylglutaconic aciduria (3-MGCA)), DHCR7 (Smith-Lemli-Opitz syndrome), HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2 deficiency), HSD17B10 (17-beta-hydroxysteroid dehydrogenase X deficiency), FKBP14 (Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss; EDSKMH) and ROGDI (Kohlschütter-Tönz syndrome). These genes have been selected because of our specific research interests in these rare and metabolic diseases. The aim of the database was to include all identified individuals with variants in these specific genes. Identical genotypes are listed multiple times if they were found in several patients, phenotypic descriptions and biochemical data are included as detailed as possible in view also of validating the proposed pathogenicity of these genotypes. For DHCR7 genetic modifier data (maternal APOE and ABCA1 genotypes) is also included. Databases are available at http://databases.lovd.nl/shared/genes and will be updated based on periodic literature reviews and submitted reports. PMID:25111118

Lanthaler, Barbara; Wieser, Stefanie; Deutschmann, Andrea; Schossig, Anna; Fauth, Christine; Zschocke, Johannes; Witsch-Baumgartner, Martina

2014-10-15

335

Application of Biomolecular Computing to Medical Science: A Biomolecular Database System for Storage, Processing & Retrieval of Genetic Information & Material  

E-print Network

recombinant DNA operations. We also utilize recent biotechnology developments (recombinant DNA technology, DNA how these queries can be executed by applying recombinant DNA operations on this Biomolecular Database DNA hybridization array technology). The paper also discusses applications of such a Biomolecular

Reif, John H.

336

Physiological Information Database (PID)  

EPA Science Inventory

EPA has developed a physiological information database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence as well as similar data for laboratory animal spec...

337

THE ECOTOX DATABASE  

EPA Science Inventory

The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

338

Search the PAQ Database  

Cancer.gov

Use this interface to search through all the physical activity-related questions in our database. See below for some tips on how to search. If you have any comments concerning this database, please e-mail David Berrigan.

339

Structural Ceramics Database  

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

340

Information storage in DNA sequences  

SciTech Connect

We seek to describe a starting point for modeling the evolution of DNA sequences within the framework of cellular automata by discussing the current understanding of genetic information storage in DNA sequences. This includes alternately viewing the role of DNA in living organisms as a simple scheme and as a complex scheme; a presentation of the extent of experimentally determined DNA sequence data present in the Los Alamos Nucleic Acid Database; and finally, a brief review of strategies for identifying and classifying patterns in DNA sequences.

Burks, C.

1983-01-01

341

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers  

PubMed Central

Background Most information on genomic variations and their associations with phenotypes are covered exclusively in scientific publications rather than in structured databases. These texts commonly describe variations using natural language; database identifiers are seldom mentioned. This complicates the retrieval of variations, associated articles, as well as information extraction, e. g. the search for biological implications. To overcome these challenges, procedures to map textual mentions of variations to database identifiers need to be developed. Results This article describes a workflow for normalization of variation mentions, i.e. the association of them to unique database identifiers. Common pitfalls in the interpretation of single nucleotide polymorphism (SNP) mentions are highlighted and discussed. The developed normalization procedure achieves a precision of 98.1 % and a recall of 67.5% for unambiguous association of variation mentions with dbSNP identifiers on a text corpus based on 296 MEDLINE abstracts containing 527 mentions of SNPs. The annotated corpus is freely available at http://www.scai.fraunhofer.de/snp-normalization-corpus.html. Conclusions Comparable approaches usually focus on variations mentioned on the protein sequence and neglect problems for other SNP mentions. The results presented here indicate that normalizing SNPs described on DNA level is more difficult than the normalization of SNPs described on protein level. The challenges associated with normalization are exemplified with ambiguities and errors, which occur in this corpus. PMID:21992066

2011-01-01

342

Querying Graph Databases  

Microsoft Academic Search

Graph data is an emerging model for representing a variety of database contexts ranging from object-oriented databases to\\u000a hypertext data. Also many of the recursive queries that arise in relational databases are, in practice, graph traversals.\\u000a In this paper we present a language for searching graph-like databases. The language permits us to express paths in a graph\\u000a by means of

Sergio Flesca; Sergio Greco

2000-01-01

343

NIST Special Database 10  

Microsoft Academic Search

This document describes the NIST fingerprint database, NIST Special Database 10. The databaseprovides a large sample of patterns for transitional fingerprint classes and classes with a low naturalfrequency of occurrence in NIST Special Database 9. The 552 fingerprint cards in NIST SpecialDatabase 10 are non-mated cards archived on a set of three CD-ROM's with the first CD-ROMcontaining 2160 fingerprint images

C. I. Watson

1993-01-01

344

Semantics of Database Transformations  

Microsoft Academic Search

. Database transformations arise in many different settings includingdatabase integration, evolution of database systems, and implementing user viewsand data-entry tools. This paper surveys approaches that have been taken to problemsin these settings, assesses their strengths and weaknesses, and develops requirementson a formal model for specifying and implementing database transformations.We also consider the problem of insuring the correctness of database transformations.In

Peter Buneman; Susan B. Davidson; Anthony Kosky

1995-01-01

345

Reviewing population studies for forensic purposes: Dog mitochondrial DNA  

PubMed Central

Abstract The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework. PMID:24453568

Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

2013-01-01

346

HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment.  

PubMed

Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the "postgenomic era": the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it. PMID:23696374

Vianello, Dario; Sevini, Federica; Castellani, Gastone; Lomartire, Laura; Capri, Miriam; Franceschi, Claudio

2013-09-01

347

The Latin American Social Medicine database  

PubMed Central

Background Public health practitioners and researchers for many years have been attempting to understand more clearly the links between social conditions and the health of populations. Until recently, most public health professionals in English-speaking countries were unaware that their colleagues in Latin America had developed an entire field of inquiry and practice devoted to making these links more clearly understood. The Latin American Social Medicine (LASM) database finally bridges this previous gap. Description This public health informatics case study describes the key features of a unique information resource intended to improve access to LASM literature and to augment understanding about the social determinants of health. This case study includes both quantitative and qualitative evaluation data. Currently the LASM database at The University of New Mexico brings important information, originally known mostly within professional networks located in Latin American countries to public health professionals worldwide via the Internet. The LASM database uses Spanish, Portuguese, and English language trilingual, structured abstracts to summarize classic and contemporary works. Conclusion This database provides helpful information for public health professionals on the social determinants of health and expands access to LASM. PMID:15627401

Eldredge, Jonathan D; Waitzkin, Howard; Buchanan, Holly S; Teal, Janis; Iriart, Celia; Wiley, Kevin; Tregear, Jonathan

2004-01-01

348

SHORT COMMUNICATION The Histone Database: A Comprehensive Resource for  

E-print Network

SHORT COMMUNICATION The Histone Database: A Comprehensive Resource for Histones and Histone Fold, National Institutes of Health, Bethesda, Maryland 2 Genome Technology Branch, National Human Genome a direct impact on DNA transcription and replication).1 Eukary- otic DNA wraps around a histone octamer

Mariño-Ramírez, Leonardo

349

Forensic DNA analysis.  

PubMed

Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

McDonald, Jessica; Lehman, Donald C

2012-01-01

350

Graph database systems  

Microsoft Academic Search

We have investigated using graphs as the foundation for database systems by developing a graph-based DBMS. We have demonstrated that: 1. Graph-based representations are useful for representing genome data. 2. A graph data model tailored to the requirements of genome data can be used as the basis of a database management system. 3. A graph database management system is a

M. Graves; E. R. Bergeman; C. B. Lawrence

1995-01-01

351

DHQ Database Revision History  

Cancer.gov

The following details all additions and revisions made to the DHQ nutrient and food database. This revision history is provided as a reference for investigators who may have performed analyses with a previous release of the database. The contents of the current database are listed in Nutrient and Dietary Constituents and Pyramid Food Groups.

352

On Database Logic  

Microsoft Academic Search

Database logic is a proposed framework for database theory which can serve the relational, hierarchical, and network approaches as first-order logic serves the relational approach. In this paper, the first m a series, the key defimuons for database logic are estabhshed, it is demonstrated how the logtc may be used to design a generahzed calculus data mampulauon language for heterogeneous

Barry E. Jacobs

1982-01-01

353

Mission and Assets Database  

NASA Technical Reports Server (NTRS)

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

354

Plant and Crop Databases  

Technology Transfer Automated Retrieval System (TEKTRAN)

Databases have become an integral part of all aspects of biological research, including basic and applied plant biology. The importance of databases continues to increase as the volume of data from direct and indirect genomics approaches expands. What is not always obvious to users of databases is t...

355

USER'S GUIDE DATABASE SYSTEM  

E-print Network

. Database Management Tools IV. Data Collection Utilities V. Data Archiving Procedures Appendix 1. Moving database system1 is an integrated set of tools which is used to collect and manage diagnostic dataUSER'S GUIDE TO THE MINGL DATABASE SYSTEM FOR TFTR Version 4.1 R. M. Wieland Plasma Physics

356

An occurence records database of French Guiana harvestmen (Arachnida, Opiliones)  

PubMed Central

Abstract This dataset provides information on specimens of harvestmen (Arthropoda, Arachnida, Opiliones) collected in French Guiana. Field collections have been initiated in 2012 within the framework of the CEnter for the Study of Biodiversity in Amazonia (CEBA: www.labex-ceba.fr/en/). This dataset is a work in progress.  Occurrences are recorded in an online database stored at the EDB laboratory after each collecting trip and the dataset is updated on a monthly basis. Voucher specimens and associated DNA are also stored at the EDB laboratory until deposition in natural history Museums. The latest version of the dataset is publicly and freely accessible through our Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=harvestmen_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/3c9e2297-bf20-4827-928e-7c7eefd9432c. PMID:25589875

Solbčs, Pierre; Grosso, Bernadette

2014-01-01

357

RefSeq microbial genomes database: new representation and annotation strategy.  

PubMed

The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks. PMID:24316578

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris; O'Neill, Kathleen; Tolstoy, Igor

2014-01-01

358

RefSeq microbial genomes database: new representation and annotation strategy  

PubMed Central

The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks. PMID:24316578

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris; O’Neill, Kathleen; Tolstoy, Igor

2014-01-01

359

GOLD: The Genomes Online Database  

DOE Data Explorer

Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

The basic tables in the GOLD database that can be browsed or searched include the following information:

  • Gold Stamp ID
  • Organism name
  • Domain
  • Links to information sources
  • Size and link to a map, when available
  • Chromosome number, Plas number, and GC content
  • A link for downloading the actual genome data
  • Institution that did the sequencing
  • Funding source
  • Database where information resides
  • Publication status and information

(Specialized Interface)

Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

360

ETC Spills Technology Databases: Oil Properties Database  

NSDL National Science Digital Library

The Environmental Technology Center of Environment Canada provides a database which contains various properties of crude oils and petroleum products. In addition to the listing of oils, the database reports properties "which will likely determine the environmental behavior and effects of spilled oil." The user may select an oil from a pull-down menu that lists 412 oils. The data are organized into tables in the following areas: Origin, API Gravity, Density, Pour Point, Dynamic Viscosity, Hydrocarbon Groups, and Distillation.

Fieldhouse, B.

361

Raintree: Tropical Plant Database  

NSDL National Science Digital Library

Hosted by Raintree, the Tropical Plant Database is authored and maintained by Board Certified Naturopath, Ms. Leslie Taylor to provide accurate information about rainforest plants and to help promote rainforest conservation. Including over 300 pages of documentation on rainforest plants and very well-organized, the Tropical Plant Database lists plants by Common name, Botanical name, Ethnic uses, and Action/disorder. The Database File for each plant includes an illustration and information about family, genus, species, common names, plant description, and more. Visitors can link to great illustrations and photos as well as web resources for each plant including Medline Abstracts, W3 TROPICOS Database, Ethnobotany Database, and Phtyochem Database among others. Plant Database File pages include references as well.

362

Database description with SDM: a semantic database model  

Microsoft Academic Search

SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. An SDM specification describes a database in terms of the kinds of entities that exist in the application environment, the classifications and groupings of

Michael M. Hammer; Dennis Mc Leod

1981-01-01

363

Database Description with SDM: A Semantic Database Model  

E-print Network

as the database model for a new kind of database management system. Key Words and Phrases: database managementDatabase Description with SDM: A Semantic Database Model MICHAEL HAMMER Massachusetts Institute of Technology and DENNIS McLEOD University of Southern California SDM is a high-level semantics-based database

McLeod, Dennis

364

Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update  

NASA Technical Reports Server (NTRS)

This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

2014-01-01

365

Comprehensive thematic T-matrix reference database: A 2013-2014 update  

NASA Astrophysics Data System (ADS)

This paper is the sixth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

2014-10-01

366

DOLOP: A Database of Bacterial Lipoproteins  

NSDL National Science Digital Library

Bacteria rely on protein-lipid combinations known as lipoproteins to glom onto surfaces, sense their surroundings, slurp up nutrients, shuttle DNA to other cells, and perform other life tasks. Researchers can analyze more than 270 of the molecules at DOLOP, a database from the Medical Research Council Laboratory of Molecular Biology in Cambridge, U.K. Entries describe each protein, indicate its size and function, and provide links to the Swiss-Prot database, where you can parse the molecule's sequence and structural features. The site also explains the synthesis of lipoproteins and describes the lipobox, a characteristic amino acid string to which lipids attach.

M. Maden Babu (MRC-Laboratory of Molecular Biology, Cambridge; )

2001-09-15

367

Women in Politics: Bibliographic Database  

NSDL National Science Digital Library

This bibliographic database currently holds 650 titles of recent works concerned with women in politics. A new addition to the Inter-Parliamentary Union's "Democracy through Partnership between Men and Women in Politics" site, "it provides bibliographic references to books, reports and journal articles on all aspects of women's participation in political life worldwide." The search mechanism allows users to specify type of document, geographic region, publishing organization, subject matter, author, title of periodical, and year of publication. Alternatively, there is also a subject keyword search. For more information about the Inter-Parliamentary Union Website, see the December 12, 1997 Scout Report.

368

Open access intrapartum CTG database  

PubMed Central

Background Cardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that. Description The intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is – on purpose – from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper. Conclusion A new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations. PMID:24418387

2014-01-01

369

The Combined Health Information Database (CHD) Online  

NSDL National Science Digital Library

A joint project of the National Institutes of Health and the Centers for Disease Control and Prevention, this unified database of bibliographic records has been available to the public since 1985, and now sports a clean new interface. There are sixteen separately maintained databases that can be searched individually or at once, ranging from AIDS Education and Alzheimers Disease to Cancer Prevention and Weight Control. The simple search interface offers a single box into which keywords are entered. The detailed search interface allows the user to specify date of publication, media type, and language, and provides multiple query boxes that may be linked together by Boolean operators. Searches return lists of matches, from which individual bibliographic records (including abstracts) may be viewed. Reprint ordering procedures are also listed. Users may also browse information on the scope and coverage of each of the sixteen databases.

1997-01-01

370

The HITRAN 2008 Molecular Spectroscopic Database  

NASA Technical Reports Server (NTRS)

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are not resolved; individual line parameters and absorption cross sections for bands in the ultra-violet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for forty-two molecules including many of their isotopologues.

Rothman, Laurence S.; Gordon, Iouli E.; Barbe, Alain; Benner, D. Chris; Bernath, Peter F.; Birk, Manfred; Boudon, V.; Brown, Linda R.; Campargue, Alain; Champion, J.-P.; Chance, Kelly V.; Coudert, L. H.; Sung, K.; Toth, R. A.

2009-01-01

371

The EMBL Nucleotide Sequence Database: major new developments  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and main- tained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collabora- tion with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization.

Guenter Stoesser; Wendy Baker; Alexandra Van Den Broek; Maria Garcia-pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan

2003-01-01

372

Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches.  

PubMed

Recent advances in sequencing and metagenomics have enabled the discovery of many novel single stranded DNA (ssDNA) viruses from various environments. We have previously demonstrated that adult dragonflies, as predatory insects, are useful indicators of ssDNA viruses in terrestrial ecosystems. Here we recover and characterise 13 viral genomes which represent 10 novel and diverse circular replication associated protein (Rep)-encoding single stranded (CRESS) DNA viruses (1628-2668nt) from Procordulia grayi and Xanthocnemis zealandica dragonfly larvae collected from four high-country lakes in the South Island of New Zealand. The dragonfly larvae associated CRESS DNA viruses have different genome architectures, however, they all encode two major open reading frames (ORFs) which either have bidirectional or unidirectional arrangement. The 13 viral genomes have a conserved NAGTATTAC nonanucleotide motif and in their predicted Rep proteins we identified the rolling circle replication (RCR) motif 1, 2 and 3, as well as superfamily 3 (SF3) helicase motifs. Maximum likelihood phylogenetic and pairwise identity analysis of the Rep amino acid sequences reveal that the dragonfly larvae novel CRESS DNA viruses share <63% pairwise amino acid identity to the Reps of other CRESS DNA viruses whose complete genomes have been determined and available in public databases and that these viruses are novel. CRESS DNA viruses are circulating in larval dragonfly populations; however, we are unable to ascertain whether these viruses are infecting the larvae directly or are transient within dragonflies via their diet. PMID:24462907

Dayaram, Anisha; Galatowitsch, Mark; Harding, Jon S; Argüello-Astorga, Gerardo R; Varsani, Arvind

2014-03-01

373

THE DRINKING WATER TREATABILITY DATABASE (Conference Paper)  

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

374

The Drinking Water Treatability Database (Poster)  

EPA Science Inventory

Drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, recogni...

375

THE DRINKING WATER TREATABILITY DATABASE (Slides)  

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

376

Plant databases and data analysis tools  

Technology Transfer Automated Retrieval System (TEKTRAN)

It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public database...

377

Toward Network Advertisement Database Management System  

Microsoft Academic Search

As the network advertisement has been developing widely, the problems, such as the fraudulent advertisements and compulsive promotions are presented, which has caused the trust of the public for advertisements to lose unceasingly and the advertisement effect to be weaken gradually. The paper proposals a scheme solving of network advertisement database management system. In the proposed NADBMS, B\\/S structure is

Aihong Liu

2009-01-01

378

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1991-1992  

NASA Technical Reports Server (NTRS)

This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 1991 through 1992. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1993-01-01

379

NASA scientific and technical publications: A catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987  

NASA Technical Reports Server (NTRS)

This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1988-01-01

380

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1989  

NASA Technical Reports Server (NTRS)

This catalog lists 190 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA scientific and technical information database during accession year 1989. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1990-01-01

381

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1987-1990  

NASA Technical Reports Server (NTRS)

This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into NASA Scientific and Technical Information Database during the year's 1987 through 1990. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1991-01-01

382

IEEE Conference Publications in Libraries.  

ERIC Educational Resources Information Center

Conclusions of surveys (63 libraries, OCLC database, University of Rhode Island users) assessing handling of Institute of Electrical and Electronics Engineers (IEEE) conference publications indicate that most libraries fully catalog these publications using LC cataloging, and library patrons frequently require series access to publications. Eight…

Johnson, Karl E.

1984-01-01

383

Database User Aids and Materials--A Study.  

ERIC Educational Resources Information Center

Based on information solicited from database producers which had files publicly available on SDC and/or Lockheed, this study is intended to help searchers assess available database support materials with regard to their cost, format, depth, and purpose. The eight assumptions addressed cover the following areas: (1) the amount of reference material…

Unruh, Betty

384

The Vocational Guidance Research Database: A Scientometric Approach  

ERIC Educational Resources Information Center

The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the use of…

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

385

Characteristics of Resources Represented in the OCLC CORC Database.  

ERIC Educational Resources Information Center

Examines the characteristics of Web resources in Online Computer Library Center's (OCLC) Cooperative Online Resource Catalog (CORC) in terms of subject matter, source of content, publication patterns, and units of information chosen for representation in the database. Suggests that the ability to successfully use a database depends on…

Connell, Tschera Harkness; Prabha, Chandra

2002-01-01

386

A catalog of new eclipsing binaries in the Kepler database  

E-print Network

In this thesis, we present a catalog of binary stars discovered in the publicly available Kepler database, none of which were included in previous such catalogs published by the Kepler science team. A brief review of other ...

Kotson, Michael Christopher

2012-01-01

387

International Regulation Database  

NSDL National Science Digital Library

Created and maintained by the Organisation for Economic Co-operation and Development (OECD), the International Regulation Database is a "comprehensive internationally-comparable set of information about the state of regulation and market structures in OECD countries." The contents of the database are derived primarily from an ad hoc questionnaire that was given to OECD member countries in 1998. The database contains over 1,100 variables for each country and includes both broad regulations dealing with product markets, such as "state control of business enterprises" and international trade and investment barriers, as well as sector-specific regulations for areas such as telecommunications, retail distribution, and electricity supply. The database must be downloaded to users's computers, and is offered in both Access and Excel versions. An eleven-page, detailed description of the database's contents, structure, and use is also available, as is a Users' Guide, which offers step-by-step instructions for manipulating the Access database.

388

Acute Toxicity Database  

NSDL National Science Digital Library

This searchable database (by species or chemical) from the US Geological Survey was initially developed in 1986 using some 4,900 acute toxicity tests (since 1969) with 410 chemicals and 66 species of aquatic animals. Two databases may be viewed online (or downloaded): the ID Database (CSV format), including Chemical ID, Chemical Name, Units of Measure, Use of Chemical, and CAS number, and Acute Toxicity Test Results Database, a CSV file with acute toxicity data by Chemical ID. Also available onsite is the "Manual of Acute Toxicity: Interpretation and DataBase for 410 Chemicals and 66 Species of Freshwater Animals." The manual describes the database structure and contents, data quality, and metadata reference information.

389

Electricity Database Files  

NSDL National Science Digital Library

The Electricity Database Files Web site from the Department of Energy's Energy Information Administration division contains several helpful resources. The site's two main categories are entitled Electric Generator Databases and Power Plant Databases, which contain more than a dozen links to related information. These include everything from an Annual Electric Generator Report, Electric Utilities Database, and a Wholesale Electric Trade Database, to a Clean Air Act Database Browser that provides information about electricity generators that must comply with the sulfur dioxide provisions of the Clean Air Act Amendments of 1990. This unique and informative collection, besides being easy to access, makes utilizing the information simple by allowing users to download the files as either Microsoft Access or Excel files.

390

TaxMan: a taxonomic database manager  

PubMed Central

Background Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes) can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. Results TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level) and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. Conclusion TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of both annotation and BLAST similarity, it ensures that all available sequence data can be brought to bear on a phylogenetic problem, but remains fast enough to cope with many thousands of records. By automatically assisting in the selection of the best subset of taxa to address a particular phylogenetic problem, TaxMan greatly speeds up the process of generating multiple sequence alignments for phylogenetic analysis. Our results indicate that an automated phylogenetic workbench can be a useful tool when correctly guided by user knowledge. PMID:17176465

Jones, Martin; Blaxter, Mark

2006-01-01

391

Space medicine research publications: 1983-1984  

NASA Technical Reports Server (NTRS)

A list of publications supported by the Space Medicine Program, Office of Space Science and Applications is given. Included are publications entered into the Life Sciences Bibliographic Database by The George Washington University as of October 1, 1984.

Solberg, J. L.; Pleasant, L. G.

1984-01-01

392

Trends in Database Research  

Microsoft Academic Search

Research in databases has played a vital role in developing information system technology and also the outcome of this research\\u000a has been very successful resulting in great potential for industry. The database industry is generating billions of dollars\\u000a of business annually. It has estimated that the database industry itself has generated $42 billion revenue in 2000 and this\\u000a market is

Mukesh K. Mohania; Yahiko Kambayashi; A. Min Tjoa; Roland Wagner; Ladjel Bellatreche

2001-01-01

393

2010 Worldwide Gasification Database  

DOE Data Explorer

The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

394

USCM Mayoral Elections Database  

NSDL National Science Digital Library

The US Conference of Mayors (USCM) (see the January 1, 1999 Scout Report) provides the Mayoral Elections Database. The database allows citizens from all 50 states and the District of Columbia to locate information on mayoral elections held in 1999. Users may search the database by city, state, political party, or name of candidate. Searches yield city name, state, party and name of election winner, percentage of votes earned by winner, and month of election. [AO

395

POW/MIA Database  

NSDL National Science Digital Library

POW/MIA Database. Library of Congress, Washington, D.C.: This database assists researchers investigating the U.S. government documents pertaining to U.S. military personnel killed, missing, or imprisoned in Southeast Asia during or after the American involvement in the Vietnam Conflict. The database is searchable by last name, country name, service branch, or keywords, and copies of desired documents may be obtained from the Library of Congress.

396

ITS-90 Thermocouple Database  

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

397

Nanotechnology with DNA DNA Nanodevices  

E-print Network

Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

Ludwig-Maximilians-Universität, München

398

DNA Profiling of Convicted Offender Samples for the Combined DNA Index System  

ERIC Educational Resources Information Center

The cornerstone of forensic chemistry is that a perpetrator inevitably leaves trace evidence at a crime scene. One important type of evidence is DNA, which has been instrumental in both the implication and exoneration of thousands of suspects in a wide range of crimes. The Combined DNA Index System (CODIS), a network of DNA databases, provides…

Millard, Julie T

2011-01-01

399

CMD: a Cotton Microsatellite Database resource for Gossypium genomics  

Microsoft Academic Search

BACKGROUND: The Cotton Microsatellite Database (CMD) http:\\/\\/www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays

Anna Blenda; Jodi Scheffler; Brian Scheffler; Michael Palmer; Jean-Marc Lacape; John Z Yu; Christopher Jesudurai; Sook Jung; Sriram Muthukumar; Preetham Yellambalase; Stephen Ficklin; Margaret Staton; Robert Eshelman; Mauricio Ulloa; Sukumar Saha; Ben Burr; Shaolin Liu; Tianzhen Zhang; Deqiu Fang; Alan Pepper; Siva Kumpatla; John Jacobs; Jeff Tomkins; Roy Cantrell; Dorrie Main

2006-01-01

400

A FLEXIBLE FRAMEWORK FOR WEB INTERFACES TO IMAGE DATABASES: SUPPORTING USER-DEFINED ONTOLOGIES AND LINKS TO EXTERNAL DATABASES  

E-print Network

AND LINKS TO EXTERNAL DATABASES Josiah Johnston, Arpun Nagaraja, Harry Hochheiser, Ilya Goldberg Image of annotated data can be linked to external data sources such as model organism databases. A case study involving publication of in-situ hybridization images cross-linked with the Mouse Gene Index is described

Kammen, Daniel M.

401

The Martian Climate Database  

NSDL National Science Digital Library

This site features access to a database of statistics that was developed in order to describe the climate and surface environment of Mars. The database provides a valuable resource for scientific studies of the Martian atmosphere. The database is based directly on output from multi-annual integrations of two General Circulation Models (GCMs) which were developed jointly at Laboratoire de Météorologie Dynamique du CNRS, Paris, and the University of Oxford, with support from the European Space Agency. The site also includes an online version of a poster that gives examples of database output, including comparisons with previous observations.

S.R. Lewis

402

A web-database of mammalian morphology and a reanalysis of placental phylogeny  

PubMed Central

Background Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny. Results The results reinforce the growing consensus regarding the extant placental mammal clades of Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel) characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria. Bayesian analyses of morphology, indels, and DNA support both a basal position for Afrotheria and the position of Cretaceous eutherians outside of crown Placentalia. Depending on treatment of third codon positions, the affinity of several fossils (Leptictis,Paleoparadoxia, Plesiorycteropus and Zalambdalestes) vary, highlighting the potential effect of sequence data on fossils for which such data are missing. Conclusion The combined dataset supports the location of the placental mammal root at Afrotheria or Xenarthra, not at Erinaceus or rodents. Even a small morphological dataset can have a marked influence on the location of the root in a combined-data analysis. Additional morphological data are desirable to better reconstruct the position of several fossil taxa; and the graphic-rich, web-based morphology data matrix presented here will make it easier to incorporate more taxa into a larger data matrix. PMID:17608930

Asher, Robert J

2007-01-01

403

CDD: NCBI's conserved domain database  

PubMed Central

NCBI's CDD, the Conserved Domain Database, enters its 15th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. PMID:25414356

Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.; Lu, Shennan; Chitsaz, Farideh; Geer, Lewis Y.; Geer, Renata C.; He, Jane; Gwadz, Marc; Hurwitz, David I.; Lanczycki, Christopher J.; Lu, Fu; Marchler, Gabriele H.; Song, James S.; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A.; Zhang, Dachuan; Zheng, Chanjuan; Bryant, Stephen H.

2015-01-01

404

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials  

PubMed Central

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics. PMID:16214744

Lorenz, Joseph G; Jackson, Whitney E; Beck, Jeanne C; Hanner, Robert

2005-01-01

405

78 FR 49730 - Collection of Information; Proposed Extension of Approval; Comment Request-Publicly Available...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Product Safety Information Database AGENCY: Consumer Product...Product Safety Information Database. The Commission will consider...information from the Office of Management and Budget (OMB). DATES...publicly available, searchable database on the safety of...

2013-08-15

406

The PROSITE database, its status in 2002  

Microsoft Academic Search

PROSITE (Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219) is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http:\\/\\/www.expasy.org\\/prosite\\/) consists of biologically significant patterns and profiles designed in such a way that with appropriate compu- tational tools it can rapidly

Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J. A. Sigrist; Kay Hofmann; Amos Bairoch

2002-01-01

407

DNA barcoding insect–host plant associations  

PubMed Central

Short-sequence fragments (‘DNA barcodes’) used widely for plant identification and inventorying remain to be applied to complex biological problems. Host–herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcode amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included—more than 10 per cent of the known Australian fauna—feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions. PMID:19004756

Jurado-Rivera, José A.; Vogler, Alfried P.; Reid, Chris A.M.; Petitpierre, Eduard; Gómez-Zurita, Jesús

2008-01-01

408

DNA barcoding insect-host plant associations.  

PubMed

Short-sequence fragments ('DNA barcodes') used widely for plant identification and inventorying remain to be applied to complex biological problems. Host-herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcodes amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included-more than 10 per cent of the known Australian fauna-feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions. PMID:19004756

Jurado-Rivera, José A; Vogler, Alfried P; Reid, Chris A M; Petitpierre, Eduard; Gómez-Zurita, Jesús

2009-02-22

409

Central Asia Active Fault Database  

NASA Astrophysics Data System (ADS)

The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late Pleistocene landforms observed near the fault trace.

Mohadjer, Solmaz; Ehlers, Todd A.; Kakar, Najibullah

2014-05-01

410

The RECONS 25 Parsec Database  

NASA Astrophysics Data System (ADS)

The REsearch Consortium On Nearby Stars (RECONS, www.recons.org) Team has been mapping the solar neighborhood since 1994. Nearby stars provide the fundamental framework upon which all of stellar astronomy is based, both for individual stars and stellar populations. The nearest stars are also the primary targets for extrasolar planet searches, and will undoubtedly play key roles in understanding the prevalence and structure of solar systems, and ultimately, in our search for life elsewhere.We have built the RECONS 25 Parsec Database to encourage and enable exploration of the Sun's nearest neighbors. The Database, slated for public release in 2015, contains 3088 stars, brown dwarfs, andexoplanets in 2184 systems as of October 1, 2014. All of these systems have accurate trigonometric parallaxes in the refereed literature placing them closer than 25.0 parsecs, i.e., parallaxes greater than 40 mas with errors less than 10 mas. Carefully vetted astrometric, photometric, and spectroscopic data are incorporated intothe Database from reliable sources, including significant original data collected by members of the RECONS Team.Current exploration of the solar neighborhood by RECONS, enabled by the Database, focuses on the ubiquitous red dwarfs, including: assessing the stellar companion population of ~1200 red dwarfs (Winters), investigating the astrophysical causes that spread red dwarfs of similar temperatures by a factor of 16 in luminosity (Pewett), and canvassing ~3000 red dwarfs for excess emission due to unseen companions and dust (Silverstein). In addition, a decade long astrometric survey of ~500 red dwarfs in the southern sky has begun, in an effort to understand the stellar, brown dwarf, and planetary companion populations for the stars that make up at least 75% of all stars in the Universe.This effort has been supported by the NSF through grants AST-0908402, AST-1109445, and AST-1412026, and via observations made possible by the SMARTS Consortium.

Henry, Todd J.; Jao, Wei-Chun; Pewett, Tiffany; Riedel, Adric R.; Silverstein, Michele L.; Slatten, Kenneth J.; Winters, Jennifer G.; Recons Team

2015-01-01

411

Identity Database 1. CyberCIEGE Identity Database  

E-print Network

Identity Database 1. CyberCIEGE Identity Database CyberCIEGE is an information assurance (IA-motivated professionals. The Identity Database scenario requires players to protect an identity database that is used issues related to protecting a centralized database that is accessed by a variety of users. Security

412

A medical database case study for reflective database access control  

Microsoft Academic Search

Reflective Database Access Control (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege in an access control matrix. RDBAC aids the management of database access controls by improving the expressiveness of policies, enabling enforcement at the database level rather than at the application level. This in turn

Lars E. Olson; Carl A. Gunter; Sarah Peterson Olson

2009-01-01

413

The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database  

PubMed Central

Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases. PMID:24228241

James, Phillip; Nateche, Farida; Wellington, Elizabeth M. H.; Hacčne, Hocine

2013-01-01

414

The world bacterial biogeography and biodiversity through databases: a case study of NCBI Nucleotide Database and GBIF Database.  

PubMed

Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases. PMID:24228241

Selama, Okba; James, Phillip; Nateche, Farida; Wellington, Elizabeth M H; Hacčne, Hocine

2013-01-01

415

Public Speaking  

NSDL National Science Digital Library

In this lesson students will evaluate famous speeches in order to identify the ways in which the speech was effective or ineffective. We will explore several websites, which present themselves as databases holding hundreds of speeches. Students will also view a video identifying ways to overcome fear of public speaking. Students will look over the websites and choose one video recorded speech from each website to go back and watch. They will then view the last website, which will remind students of what they should be looking in each type of speech. After being reminded of the qualities of each type of speech, students will be given a chart to fill out. Students will then go back to each website and view the videos which they have previouisly chosen. As students watch the speeches, they will note the ways in which the speaker meets the requirements for a quality speech, i.e. eye contact, number of vocal fillers used, vocal pitch, appearance, etc. They will record this information of their charts. First let's learn about American Rhetoric Now let's take a look at this film on conquering fear of public speaking Conquering Fear of Public Speaking Now let's take a look at Speaking Now let's take a look at Speech Club Now let's take a look at Study Great Speaches Now let's take a look at Study Sphere Public Speaking ...

Ms.Maxwell

2011-10-27

416

Proposals that the International Committee on Systematics of Prokaryotes establish a public database of validly published names and that the Bacteriological Code be amended to change the prescription for citation of validly published names.  

PubMed

It is proposed that the International Committee on Systematics of Prokaryotes formally maintain a readily accessible database of validly published names and that Rule 33b of the International Code of Nomenclature of Bacteria be revised to allow a new, abbreviated, format as the sole method by which authors indicate validation of previously published names. PMID:17473278

Watson, D R W; Young, J M

2007-05-01

417

SQL databases v. NoSQL databases  

Microsoft Academic Search

The Communications Web site, http:\\/\\/cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of Communications, we'll publish excerpts from selected posts.twitterFollow us on Twitter at http:\\/\\/twitter.com\\/blogCACMMichael Stonebraker considers several performance arguments in favor of NoSQL databases---and finds them insufficient.

Michael Stonebraker

2010-01-01

418

Automating database management for distributed database systems  

NASA Astrophysics Data System (ADS)

The management of large databases can be a time consuming and tedious task without tools to automate the process. In order to facilitata the process, a database design philosophy which is consistent with application objectives must be adopted. The Planetary Plasma Interactions (PPI) Node of the Planetary Data System (PDS) provides users with a software application which allows for rapid retrieval (for examination or extraction) of datasets which are distributed and which may exist in more than one location simultaneously. In addition, the application software, which interacts with both a local and a centralized database management system (dbms) via a client-server architecture, also is distributed. The basic problem lies in keeping all of the information current in a dynamic data environment so that the application software, regardless of its location, can access any data in the system with the greatest possible throughput. In addressing this problem the PDS/PPI Node has adopted a standardized architecture [2] and has chosen to package data management information with the data themselves as a set of detached relational flatfiles. At the PDS/PPI Node automated dbms tools are being developed which update both local and central management systems by using the information provided along with the datasets. This information can be stored in any relational database system or it can be accessed and manipulated outside of a dbms. Science data are not maintained under direct dbms control.

Joy, Steven P.; King, Todd A.; Walker, Raymond J.

1993-08-01

419

Biological Macromolecule Crystallization Database  

National Institute of Standards and Technology Data Gateway

SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

420

Pharmacoepidemiology and Healthcare Databases  

Cancer.gov

These databases can be used to access national and international data that can help answer some of the outstanding questions of cancer-related outcomes (positive or negative) associated with pharmaceuticals. Some of the databases are linked to a table of pharmacoepidemiology data elements, which provides a snapshot of the material contained therein.

421

Atomic Spectra Database (ASD)  

National Institute of Standards and Technology Data Gateway

SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

422

Dictionary as Database.  

ERIC Educational Resources Information Center

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Painter, Derrick

1996-01-01

423

PAN Pesticide Database  

NSDL National Science Digital Library

The Pesticide Action Network (PAN) Pesticide Database is your one-stop location for toxicity and regulatory information for pesticides. This is a comprehensive search enabled database of pesticide chemicals and also trade names. An easy to navigate sidebar takes you through toxicity, uses, registration, company, and distributor. Other links take you to less toxic alternatives, and pesticide tutorial and references.

0000-00-00

424

A Quality System Database  

NASA Technical Reports Server (NTRS)

A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

2010-01-01

425

Assignment to database industy  

NASA Astrophysics Data System (ADS)

Various kinds of databases are considered to be essential part in future large sized systems. Information provision only by databases is also considered to be growing as the market becomes mature. This paper discusses how such circumstances have been built and will be developed from now on.

Abe, Kohichiroh

426

Criticality safety database  

SciTech Connect

The Nuclear Criticality Safety (NCS) Database is being developed by OSTI at the request of NE-74 to help workers in the area of nuclear criticality safety to accomplish their mission. It is a bibliographic database resident on the OSTI VAX cluster, and can be searched by BASIS software.

Beasley, M.; Rutkowski, R.

1994-09-01

427

NISt Chemical Kinetics Database  

NSDL National Science Digital Library

The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these.

428

Database Reviews: Legal Information.  

ERIC Educational Resources Information Center

Detailed reviews of two legal information databases--"Laborlaw I" and "Legal Resource Index"--are presented in this paper. Each database review begins with a bibliographic entry listing the title; producer; vendor; cost per hour contact time; offline print cost per citation; time period covered; frequency of updates; and size of file. A detailed…

Seiser, Virginia

429

HIV Structural Database  

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

430

Steam Properties Database  

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

431

Toward unification of taxonomy databases in a distributed computer environment  

SciTech Connect

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomy databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.

Kitakami, Hajime [Hiroshima City Univ. (Japan); Tateno, Yoshio; Gojobori, Takashi [National Institute of Genetics, Shizuoka-Ken (Japan)

1994-12-31

432

DNA microarray (spot) .  

E-print Network

1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

433

Cascadia Tsunami Deposit Database  

USGS Publications Warehouse

The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

2003-01-01

434

[Glaucoma Service Database].  

PubMed

We present the common problems related to clinical databases. The Glaucoma Service Database created in our clinic is an attempt of developing the optimal medical database. The system organizes our repository of clinical data. It consist of 3 modules: 1) the users list with predefined privileges and rights, 2) lists of coded data for further use, that facilitate filling in the fields, 3) clinical details of all patients. The user interface of our database is very simply, thus it is very easy to use it even by unskilled staff. The accuracy of data is protected by system's internal algorithms. It could be used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation and decision analysis. Data from Glaucoma Service Database can also help in the management of health service. PMID:14969171

Jamrozy-Witkowska, Agnieszka M; Witkowski, Tomasz; Krzyzanowska, Patrycja

2003-01-01

435

Illinois State Archives: Database of Illinois Civil War Veterans  

NSDL National Science Digital Library

This database from the Illinois State Archives "indexes the first eight volumes of the nine volume publication, Report of the Adjutant General of the State of Illinois." The publication is drawn from the original rosters maintained during the Civil War by the Adjutant General. In addition to the names of approximately 250,000 men organized into 175 regiments, this searchable database also provides histories of the Illinois units and regiments. The database was created and donated to the Illinois State Archives by amateur genealogist Fred Delap of Kansas, Illinois.

436

Functional ceramic materials database: an online resource for materials research.  

PubMed

We present work on the creation of a ceramic materials database which contains data gleaned from literature data sets as well as new data obtained from combinatorial experiments on the London University Search Instrument. At the time of this writing, the database contains data related to two main groups of materials, mainly in the perovskite family. Permittivity measurements of electroceramic materials are the first area of interest, while ion diffusion measurements of oxygen ion conductors are the second. The nature of the database design does not restrict the type of measurements which can be stored; as the available data increase, the database may become a generic, publicly available ceramic materials resource. PMID:18232678

Scott, D J; Manos, S; Coveney, P V; Rossiny, J C H; Fearn, S; Kilner, J A; Pullar, R C; Alford, N Mc N; Axelsson, A-K; Zhang, Y; Chen, L; Yang, S; Evans, J R G; Sebastian, M T

2008-02-01

437

Database Constraints Applied to Metabolic Pathway Reconstruction Tools  

PubMed Central

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

438

Database constraints applied to metabolic pathway reconstruction tools.  

PubMed

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

439

Protein-protein interaction databases: keeping up with growing interactomes.  

PubMed

Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction data. Protein-protein interactions have been retrieved from six major databases, integrated and the results compared. The six databases (the Biological General Repository for Interaction Datasets [BioGRID], the Molecular INTeraction database [MINT], the Biomolecular Interaction Network Database [BIND], the Database of Interacting Proteins [DIP], the IntAct molecular interaction database [IntAct] and the Human Protein Reference Database [HPRD]) differ in scope and content; integration of all datasets is non-trivial owing to differences in data annotation. With respect to human protein-protein interaction data, HPRD seems to be the most comprehensive. To obtain a complete dataset, however, interactions from all six databases have to be combined. To overcome this limitation, meta-databases such as the Agile Protein Interaction Database (APID) offer access to integrated protein-protein interaction datasets, although these also currently have certain restrictions. PMID:19403463

Lehne, Benjamin; Schlitt, Thomas

2009-04-01

440

IPD—the Immuno Polymorphism Database  

PubMed Central

The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

2013-01-01

441

ECMDB: the E. coli Metabolome Database.  

PubMed

The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ?1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry. PMID:23109553

Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S

2013-01-01

442

Complex Carbohydrate Research Center Spectral Databases  

NSDL National Science Digital Library

Dr. William York of the Complex Carbohydrate Research Center has created these two databases with scientific input from others at the University of Georgia. The Xyloglucan NMR Database consists of a searchable table of the ?H-NMR chemical shifts of xyloglucan oligoglycosyl alditols. Xyloglucans are highly branched polymers with a cellulosic backbone (i.e., consisting of b-(1,4)-linked D-glucosyl residues). The basis for the most commonly used nomenclature for xyloglucan structures comes from the linear array of glycosyl side chains that many of the backbone residues bear. The Partially Methylated Alditol Acetate (PMAA) Database shows the molecular structures of PMAAs derived from Hexopyranosyl, Pentopyranosyl, and Pentofuranosyl Residues. Users view the structures by gliding the mouse over a table. The PMAA Database also says that electron-impact mass spectra are available, but at the time of publication, these links weren't working. The Xyloglucan database comes with overviews, search guides, and nomenclature information. The PMAA database has a help page. Both require a free login.

York, William .

443

Hierarchical schemata for relational databases  

Microsoft Academic Search

Most database design methods for the relational model produce a flat database, that is, a family of relations with no explicit interrelational connections. The user of a flat database is likely to be unaware of certain interrelational semantics. In contrast, the entity-relationship model provides schema graphs as a description of the database, as well as for navigating the database. Nevertheless,

Y. Edmund Lien

1981-01-01

444

Corruption of genomic databases with anomalous sequence.  

PubMed Central

We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not restricted to one type of vector or to a single mechanism. Many minor instances may have been the result of simple editing errors, but some entries contained large blocks of vector sequence that had been incorporated by contamination or other accidents during cloning. Some cases involved unusual rearrangements and areas of vector distant from the normal insertion sites. Matches to vector were found in 0.23% of 20,000 sequences analyzed in GenBank Release 63. Although the possibility of anomalous sequence incorporation has been recognized since the inception of GenBank and should be easy to avoid, recent evidence suggests that this problem is increasing more quickly than the database itself. The presence of anomalous sequence may have serious consequences for the interpretation and use of database entries, and will have an impact on issues of database management. The incorporated vector fragments described here may also be useful for a crude estimate of the fidelity of sequence information in the database. In alignments with well-defined ends, the matching sequences showed 96.8% identity to vector; when poorer matches with arbitrary limits were included, the aggregate identity to vector sequence was 94.8%. PMID:1614861

Lamperti, E D; Kittelberger, J M; Smith, T F; Villa-Komaroff, L

1992-01-01

445

PlantGDB, plant genome database and analysis tools  

Microsoft Academic Search

PlantGDB (http:\\/\\/www.plantgdb.org\\/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that repre- sent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis

Qunfeng Dong; Shannon D. Schlueter; Volker Brendel

2004-01-01

446

Publicity and public relations  

NASA Technical Reports Server (NTRS)

This paper addresses approaches to using publicity and public relations to meet the goals of the NASA Space Grant College. Methods universities and colleges can use to publicize space activities are presented.

Fosha, Charles E.

1990-01-01

447

ResPlan Database  

NASA Technical Reports Server (NTRS)

The main project I was involved in was new application development for the existing CIS0 Database (ResPlan). This database application was developed in Microsoft Access. Initial meetings with Greg Follen, Linda McMillen, Griselle LaFontaine and others identified a few key weaknesses with the existing database. The weaknesses centered around that while the database correctly modeled the structure of Programs, Projects and Tasks, once the data was entered, the database did not capture any dynamic status information, and as such was of limited usefulness. After the initial meetings my goals were identified as follows: Enhance the ResPlan Database to include qualitative and quantitative status information about the Programs, Projects and Tasks Train staff members about the ResPlan database from both the user perspective and the developer perspective Give consideration to a Web Interface for reporting. Initially, the thought was that there would not be adequate time to actually develop the Web Interface, Greg wanted it understood that this was an eventual goal and as such should be a consideration throughout the development process.

Zellers, Michael L.

2003-01-01

448

Hazard Analysis Database Report  

SciTech Connect

The Hazard Analysis Database was developed in conjunction with the hazard analysis activities conducted in accordance with DOE-STD-3009-94, Preparation Guide for U S . Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, for HNF-SD-WM-SAR-067, Tank Farms Final Safety Analysis Report (FSAR). The FSAR is part of the approved Authorization Basis (AB) for the River Protection Project (RPP). This document describes, identifies, and defines the contents and structure of the Tank Farms FSAR Hazard Analysis Database and documents the configuration control changes made to the database. The Hazard Analysis Database contains the collection of information generated during the initial hazard evaluations and the subsequent hazard and accident analysis activities. The Hazard Analysis Database supports the preparation of Chapters 3 ,4 , and 5 of the Tank Farms FSAR and the Unreviewed Safety Question (USQ) process and consists of two major, interrelated data sets: (1) Hazard Analysis Database: Data from the results of the hazard evaluations, and (2) Hazard Topography Database: Data from the system familiarization and hazard identification.

GRAMS, W.H.

2000-12-28

449

Calculating economic indexes per household and censal section from official Spanish databases  

E-print Network

) with information on consumption by household of over 300 products. Both databases are published by the NationalCalculating economic indexes per household and censal section from official Spanish databases Sonia clients. Public databases offer information about households and families. However, the non

Malerba, Donato

450

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse  

Microsoft Academic Search

The Mouse Genome Database (MGD) is a comprehen- sive public database of mouse genomic, genetic and phenotypic information (http:\\/\\/www.informatics.jax.org ). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data,

Judith A. Blake; Janan T. Eppig; Joel E. Richardson; Muriel T. Davisson

2000-01-01

451

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness  

E-print Network

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness Melanie Dulong de and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain

Paris-Sud XI, Université de

452

Release of ToxCastDB and ExpoCastDB databases  

EPA Science Inventory

EPA has released two databases - the Toxicity Forecaster database (ToxCastDB) and a database of chemical exposure studies (ExpoCastDB) - that scientists and the public can use to access chemical toxicity and exposure data. ToxCastDB users can search and download data from over 50...

453

A Bimodal Face and Body Gesture Database for Automatic Analysis of Human Nonverbal Affective Behavior  

Microsoft Academic Search

To be able to develop and test robust affective multimodal systems, researchers need access to novel databases containing representative samples of human multi-modal expressive behavior. The creation of such databases requires a major effort in the definition of representative behaviors, the choice of expressive modalities, and the collection and labeling of large amount of data. At present, public databases only

Hatice Gunes; Massimo Piccardi

2006-01-01

454

Significant Earthquake Database  

NSDL National Science Digital Library

The Significant Earthquake Database is a global digital database containing information on more than 5,000 destructive earthquakes from 2150 B.C. to the present. Users can access these data in two different ways: via a two-volume CD collection, or on-line. Users searching on-line can query the database via the following parameters: the year of the event, geographical coordinates (latitude and longitude), country, state or province, magnitude, intensity, focal depth, number of deaths, and damage amount. A list of applicable earthquakes is then displayed.

455

Household Products Database  

NSDL National Science Digital Library

Users will find important and possibly life-saving information on over 4,000 household products in this online database from the National Library of Medicine's Specialized Information Services. The database allows users to find out what a product contains, potential health effects, and safety and handling information. Users can quickly and easily search the database by product name, ingredients, or symptom. The products search seems to be the most user-friendly, as it is organized alphabetically and by general category, e.g. home maintenance, personal care/use, auto products, and so on.

456

World Cave Database  

NSDL National Science Digital Library

The World Cave Database was created by Eric Madelaine of the French Research Institute for Computer Science and Automatic Control. Users can browse the database by depth, length, or an alphabetical listing of the caves, and can search the nearly 1000 entries by keyword. All included caves are 300 meters deep and 3 kilometers long and larger, including the longest, which is the Mammoth Cave system in the US that is known to be 563,270 meters long. After getting used to the somewhat cryptic layout of cave listings, users should find the database a useful and informative resource.

457

Phase Equilibria Diagrams Database  

National Institute of Standards and Technology Data Gateway

SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

458

World Biodiversity Database  

NSDL National Science Digital Library

The World Biodiversity Database, provided by ETI BioInformatics, seeks to document all presently known species (about 1.7 million) and to make this important biological information worldwide accessible. This continually growing database provides "taxonomic information, species names, synonyms, descriptions, illustrations and literature references, as well as online identification keys and interactive geographical information systems." The searchable database can be explored using an expandable tree of taxonomic kingdoms or by typing in a common or scientific name. Both educators and students should find this site easy to navigate, informative, and useful.

459

Hybrid Terrain Database  

NASA Technical Reports Server (NTRS)

A prototype hybrid terrain database is being developed in conjunction with other databases and with hardware and software that constitute subsystems of aerospace cockpit display systems (known in the art as synthetic vision systems) that generate images to increase pilots' situation awareness and eliminate poor visibility as a cause of aviation accidents. The basic idea is to provide a clear view of the world around an aircraft by displaying computer-generated imagery derived from an onboard database of terrain, obstacle, and airport information.

Arthur, Trey

2006-01-01

460

The Press Freedom Database  

NSDL National Science Digital Library

Developed by the Committee to Protect Journalists (CPJ), The Press Freedom Database contains case histories of documented press freedom violations against journalists and media organizations worldwide as well as annual CPJ reports on the violations in specific countries and regions. The case histories document the circumstances in which journalists have been attacked, killed, expelled, censored, harassed, threatened, and/or imprisoned. The database is searchable by journalist name, news organization, type of organization, date, country, or region. Currently, the database, which is updated weekly, contains over 2,000 reports of press freedom violations, spanning from 1993 to the present.

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